Nine-year-old Claudia MacTeer and her ten-year-old sister, Frieda MacTeer, live in an old house in Loraine, Ohio. It is 1941, near the end of the Great Depression, and their family struggles to make ends meet. Although there is a tremendous sense of love in their home, their mother, Mrs. MacTeer, is strict and punishes them often, but out of a sense of concern and love for her children. Their father works hard to keep the family afloat. To help financially, the MacTeer's take in a boarder named Henry Washington, who the girls call Mr. Henry. They later take in a young girl named Pecola Breedlove because her father, Cholly Breedlove, burned her family's house down and ended up in jail. Claudia and Frieda like Pecola, but feel sorry for her. Pecola and Frieda love Shirley Temple because of her beauty, which stems from her white features, but Claudia disagrees with them.
Eventually, Pecola moves back into the storefront apartment where her family lives, and her life continues to be hard. Her father is an abusive alcoholic, and her mother is neglectful and self-righteous. Her parents fight on a regular basis, and these altercations lead to physical violence. Pecola's brother, Samuel, copes with the violence by running away, but Pecola, being a young black girl, is unable to escape. She believes she is fated to live her sad life because she is ugly, which is confirmed by the way she is treated in the community. She prays for blue eyes because they will make her beautiful and allow her to see the world differently.
The reader learns that Pecola's parents have both had tragic lives, which has led to their dysfunction as adults. Her father, Cholly Breedlove, was abandoned as a baby and later turned away by his father after searching him out. During Cholly's first sexual experience, two white men stumble upon him and the girl he was with and force him to continue the sexual act as they watch. This humiliating incident leads Cholly to develop a hatred for women. He lives a dangerously free life, and feels tied down after getting married. Pecola's mother, Mrs. Breedlove, has a lame foot and has always felt isolated and ugly. As a young woman, she loses herself in movies. The beautiful white actresses exacerbate her belief that she is ugly. After having children, she takes on the role of a martyr, believing her relationship with Cholly is a cross she must bear as a good Christian woman. She works for a white family, and spending time in their home makes her despise her own.
One day during the spring of 1941, Cholly returns home drunk and finds Pecola washing dishes. He experiences a fury of emotions as he watches her. At first, he feels tenderness and hatred fueled by guilt. He knows he is unable to care for her, and hates her for loving him. He rapes Pecola, and leaves her on the kitchen floor. Afterward, Mrs. Breedlove beats Pecola when she learns of the rape. In an act of desperation, Pecola visits Soaphead Church, a local charlatan who claims he can work miracles, and asks for blue eyes. Soaphead Church tricks Pecola into poisoning a dog he has long wanted to kill, stating that if the dog acts funny it is a sign she will receive her wish.
When summer arrives, Claudia and Frieda begin selling marigold seeds to save for a new bike. As they make their way around the neighborhood, they learn that Pecola has been impregnated by her father. Unlike the rest of the community, the girls want the baby to live. They sacrifice the money they have made, burying it by Pecola's house, and plant the remaining marigold seeds in their backyard. They believe that if the marigold seeds grow, their prayers have been answered and the baby will live. In the end, however, the seeds do not grow and Pecola's baby dies. Afterward, Pecola goes mad, and in in her psychosis, believes she has received blue eyes. The community disowns her, and from then on she lives isolated in her own world.