In the 1920s, twenty-year-old Lena Grove hitches a wagon ride to Jefferson, Mississippi. She's pregnant and in search of Lucas Burch, the father of her baby. On the way into town, the house of a town outcast, Joanna Burden, is on fire. Lena eventually learns that there is no one in Jefferson named Burch, but that there is a fellow named Byron Bunch. Bunch, a worker at the local planing mill, talks to Lena, telling her stories about a stranger in town named Joe Brown. Once Byron confirms that Joe Brown has a white scar on his face, Lena knows that this Joe Brown is the father of her baby, so she settles into town to try to find him. But Byron falls in love with Lena right after meeting her, and vows (to himself and the local Reverend Hightower) to protect her and see her through the pregnancy, with or without this Joe Brown fellow.
Through flashback, the narrator recounts the lives of Joe Christmas and Reverend Hightower. Joe Christmas was dropped off at an orphanage on Christmas day, as an infant. When he is five years old, Joe accidentally witnesses the dietician having sex with a doctor at the orphanage. The dietician freaks out, becoming convinced that Joe is going to tell on her, and so she plots to have him removed from the orphanage. She tells Joe that he is part black, and that she's going to get him kicked out of the orphanage. Instead, she sets Joe up with a strict religious couple named the McEacherns.
Mr. McEachern is a Calvinist who believes that hard labor and obedience are the only ways to assure salvation. He beats Joe regularly and does not allow much joy or laughter into the young boy's life. Soon, Joe begins to have sex with a prostitute named Bobbie who lives in town. He sells a cow that McEachern gave him and uses the money to buy a brand new suit, so he can take Bobbie to a local dance. McEachern finds the suit and follows Joe when he sneaks out of the house. When he shows up to the dance, Joe hits him over the head with a chair, possibly killing him. He steals money from Mrs. McEachern and runs away from home, never to see either of his foster parents again.
Christmas drifts for years, sleeping with various women and trying to deal with his racial identity. He arrives in Jefferson and begins working at the planing mill with Byron Bunch and other local men. Christmas takes up residence in a cabin owned by Joanna Burden, a white woman from a long line of local abolitionists. Due to her radical views on racial equality, Miss Burden is an outcast in the town of Jefferson. Miss Burden and Christmas begin a tortured affair that involves him sneaking into her house at night; sometimes they have physical fights. Christmas quits his job at the planing mill when he starts selling whiskey illegally; he takes another stranger in town, Joe Brown, as his business partner, and invites that Joe to move into Burden's cabin with him. When Miss Burden tries to make Christmas become more religious, though, he starts hating her, plotting her murder.
Reverend Gail Hightower's story is also revealed in flashback. Hightower came to Jefferson because his great-grandfather, a member of the Confederate army, was murdered there. He's therefore obsessed with Jefferson, which is his sole reason for coming to town. None of the parishioners approve of his sermons, which he delivers bombastically and egotistically, without regard for his parish. After years of being ignored, his wife begins having affairs with other men in Memphis. One day, she's found dead, having jumped or been pushed out of a hotel window in Memphis. Hightower is defrocked and forced to resign from the church after this, and becomes a town outcast.
In the present, one night, Joanna tries to shoot Christmas with a pistol; he retaliates by murdering her with a razor and nearly decapitates her. Miss Burden's nephew offers a $1,000 reward for the capture of her murderer. Soon after the reward is announced, Joe Brown comes forward and claims that Christmas is the killer. Christmas evades the police for days, but eventually they find him in Mottstown.
In Mottstown there lives a strange couple named the Hineses. When Joe Christmas is arrested downtown, Mr. and Mrs. Hines both have strange reactions to seeing him. When he is driven off to Jefferson for his trial, the couple follows him there. When they arrive, Mrs. Hines tells Reverend Hightower that Joe Christmas is her grandson. Years ago, she reports, her daughter Milly got knocked up by a carnival worker who claimed he was Mexican. Doc Hines, however, believed differently, becoming convinced that the man was actually black. This enraged him, and he murdered Milly's lover and let her die during childbirth. Doc Hines kidnapped the baby and dropped him off at a white orphanage, telling his wife that the baby was dead.
Meanwhile, Byron arranges for Joe Brown and Lena Grove to finally meet. Brown freaks out and jumps out of the cabin window, escaping police custody. Byron tracks him down and the men fight; Joe Brown wins and jumps on a passing train, leaving Jefferson.
Joe Christmas escapes from police custody and is hunted, and ultimately killed, by a white supremacist named Percy Grimm. Grimm shoots and castrates Christmas. Lena Grove and Byron Bunch travel together through Tennessee with Lena's baby, still in search of Joe Brown.