Lena Grove, whose parents are dead, goes to live with her brother. While there, she gets pregnant by a man named Lucas Burch, who runs out on her but not before saying that he'll send for Lena once he finds a town in which they can settle down. Hearing no word from Lucas for a long time, the pregnant Lena walks from Alabama into Mississippi looking for him. Along the way she hears that Lucas might be in Jefferson, so she walks toward that town. On the day she arrives in Jefferson, an old plantation house owned by Joanna Burden is on fire. We later learn that Joe Christmas, who lived in an old slave cabin on the plantation and was having a sexual relationship with Joanna, is accused of the murder. The Jefferson townspeople seem more angry that Joe is part black and has killed a white woman than they are about it being Joanna who was murdered.
Flashback three years earlier to the Jefferson planing mill where a man named Byron Bunch works; Byron will become one of the main characters — and a primary narrator — in the novel. A man named Joe Christmas shows up looking for work and is hired, followed soon thereafter by a man named Joe Brown being hired. Christmas and Brown work together and form a relationship about which the other workers are unsure. Brown lets it be known that Christmas used to run a whiskey distillery; it's unclear if Christmas still runs it. But the talk is that Christmas still does, and that Brown delivers the whiskey to whomever will buy it. Christmas quits the planing mill; Brown quits soon thereafter. We learn that Christmas — and perhaps Brown as well — supposedly lives in an old slave quarter on the grounds of an old plantation owned by Miss Joanna Burden. Burden's family had moved to Jefferson from the north during Reconstruction; Burden purportedly remains a Yankee — which in Jefferson means befriending blacks.
Byron Bunch is working alone at the planing mill when Lena Grove shows up looking for Lucas Burch. Byron and Lena strike up a conversation, during which Byron lets slip that Joe Brown is an alias of Lucas Burch's. Byron is disappointed because he has started to have affections for Lena.
The story recounts how Reverend Gail Hightower and his wife came to Jefferson long ago when Hightower was hired by a Jefferson Presbyterian church to be its minister. Oftentimes Hightower's wife leaves Jefferson supposedly to visit her family, but one day a woman from Jefferson who is in Memphis shopping sees Mrs. Hightower, and Jefferson soon begins gossiping about why Mrs. Hightower regularly visits Memphis. Eventually she is institutionalized, and once released returns to be with her husband in Jefferson. However, she soon again regularly visits Memphis and eventually dies after falling through a hotel window; she was in the hotel with a man with whom she had registered as husband and wife. The sensationalism of Reverend Hightower's wife having been in a Memphis hotel with another man turns Jefferson against Hightower, and eventually he is forced to resign his position from the church. The town tries to force him to leave Jefferson altogether, but he refuses. The furor eventually dies down, but Hightower is forever regarded as damned by the people of Jefferson.
Byron Bunch visits Hightower and narrates how the Burden house has burned down. Miss Burden is dead from her neck being cut, and it appears that the fire was set to cover up the murder. Brown is questioned by the sheriff and claims that Christmas and Miss Burden have been sleeping with one another; even more shocking to the sheriff is Brown's assertion that Christmas is part black. It's unclear how truthful Brown is in relating the details concerning Christmas, Miss Burden, and the fire.
The story then flashes back even farther when Joe Christmas was five years old and living in an orphanage, and he inadvertently caught the dietician and another orphanage employee having sex. Joe thinks he's in trouble because he was eating a mouthful of toothpaste in the dietician's room; the dietician thinks that Joe will tell that he saw her and the man together. The dietician contrives to get Joe sent to an orphanage for black children rather than remaining at the white children's orphanage. Eventually, a man named McEachern adopts Joe and takes him home; McEachern is unaware that Joe is part black.
Time passes, and Joe eventually grows into a teenager. At seventeen, he begins sneaking out of the McEachern house and meeting a waitress named Bobbie from town. Their relationship is sexual. Joe is more serious — and naïve — about their relationship than Bobbie is. McEachern begins to suspect that Joe is sneaking out of the house and one night sees Joe go into the stable, where Joe keeps a suit to wear when meeting Bobbie. A car picks up Joe, and McEachern follows on his horse. McEachern discovers Joe and Bobbie at a dance and begins yelling at Bobbie. Joe strikes McEachern with a chair. Bobbie runs from the dance, and Joe runs home to get the secret money that Mrs. McEachern has been hiding from her husband but not from Joe. Joe goes to where Bobbie lives, intending that he and Bobbie will run away together and get married. But the couple with whom Bobbie lives over the restaurant and a nameless man are preparing to leave town with Bobbie; all of them fear that Joe has killed McEachern and that the police will soon show up on their doorstep. Joe doesn't truly understand what's happening. The stranger repeatedly strikes Joe until Joe is close to losing consciousness.
Following his losing Bobbie, Joe runs away. For fifteen years he wanders, traveling between Chicago, Detroit, and Mexico, and finally heading into Mississippi. He happens upon the Burden house and breaks in to steal food. Joe is discovered by Miss Burden, who doesn't seem upset that Joe has broken into her kitchen. In fact, Miss Burden allows Joe to stay in an old slave cabin on her property. One night he enters the Burden house unannounced, goes to her bedroom, and has sex with her. But then, troubled with himself, Joe avoids her until one day he finds her in his cabin, where she tells Joe the story of herself and her ancestors.
Joe and Joanna's relationship goes through various phases. At one point, Joanna says that she's pregnant — although she is not. Toward the end of their relationship, Joanna tries to get Joe to go to a school for blacks and then become a lawyer, but Joe will not do these things, in part because that would mean he would first have to acknowledge that he is part black. The last phase of their relationship involves Joanna trying to get Joe to pray with her, but Joe refuses. Joanna suggests that perhaps both she and Joe should kill themselves, and not too long thereafter Joe kills Joanna.
The sheriff hunts for Joe but is unable to track him down. Byron Bunch speaks to Hightower and reveals that he has taken Lena to live in the cabin that Lucas Burch and Joe Christmas lived in on the Burden plantation. Joe, continually avoiding capture by the Jefferson sheriff, eventually hitches a ride going to Mottstown, which is not too far from Jefferson.
Joe is caught in Mottstown without putting up a struggle. During Joe's capture, Uncle Doc Hines is downtown and hears Joe's name being said by the townspeople. He runs up to the crowd holding Joe and begins yelling that Joe should be killed immediately. Later, Mrs. Hines asks her husband what he did with Milly's baby — meaning Joe Christmas; eventually we learn that Joe Christmas is the Hines' grandson, born to their daughter, Milly. The sheriff from Jefferson arrives in Mottstown and takes custody of Joe. Uncle Doc and Mrs. Hines buy two train tickets for Jefferson.
Back in Jefferson, Byron brings Doc and Mrs. Hines to Hightower's house, where Doc and Mrs. Hines individually recount Joe's history: The Hines' daughter, Milly, had sex with a black man from a traveling circus and got pregnant. Hines killed the man, and Milly eventually died giving birth to Joe. Hines took Joe without Mrs. Hines' knowledge and deposited him on an orphanage's doorstep. During the next five years, Hines watched Joe grow; Mrs. Hines had no idea if Joe was even alive. Once the Hines have finished relating Joe's history, Byron asks Hightower if Hightower will lie and say that Joe was with him when Joanna Burden was killed, thereby providing Joe an alibi. Hightower adamantly refuses.
Byron gets Hightower to come to the cabin in which Lena is staying because Lena is about to give birth. Doc and Mrs. Hines are there as well. Hightower helps Lena gives birth to a boy, and then returns home. Later, he again returns to the cabin and finds Lena and her son alone. Lena explains that Byron asked her to marry him and that she said no. Hightower learns that Byron has quit his job at the planing mill and is downtown at the courthouse.
Bryon talks the sheriff into taking Lucas Burch out to the cabin to show Lena and the baby to him. Lucas is surprised to see Lena, as well as the baby. He begins his usual deceitful banter about his wanting to take care of Lena and their child, but he's waiting on money and has enemies who don't want him to get it. He again walks out on Lena, slipping through a back window of the cabin so that the deputy sheriff waiting at the front won't see him. Byron spies Lucas leaving the cabin and follows him, eventually catching up to Lucas by the train tracks that run outside of Jefferson. Byron fights Lucas and is beaten — as he guessed he would be. Byron watches as Lucas jumps onto a train and disappears. While Byron is walking back to the cabin, a man in a passing wagon tells Byron that Joe has been killed.
We learn that as the deputy sheriff was leading Joe through the town square, Joe escaped. A young man named Percy Grimm, who had organized men to guard the courthouse, jail, and square, followed Joe and eventually saw Joe run into Hightower's house. Earlier, Joe's grandmother, Mrs. Hines, had visited Joe in jail and told Joe about Hightower. Over Hightower's assertion that Joe was with him the night Joanna Burden was murdered, Grimm repeatedly shoots Joe, and then castrates him with a butcher knife. Joe dies.
At the end of the novel, Lena is again on the road, only this time she has Byron Bunch and her baby with her. Bunch wants to marry Lena, but Lena seems consumed with finding Lucas Burch — plus she likes traveling.