The novel consists of five chapters, titled "Thousand Cranes", "The Grove in the Evening Sun", "Figured Shino", "Her Mother's Lipstick" and "Double Star".
28-year-old Tokyo office worker Kikuji attends the tea ceremony lesson of Miss Chikako Kurimoto, with whom his deceased father once had a short-lived affair. He still vividly remembers a large naevus on her chest, which he once saw as a child. Kikuji is impressed by the beauty of one of Miss Kurimoto's pupils, Yukiko Inamura, who carries a furoshiki which bears a pattern of the thousand cranes of the novel's title. The tea ceremony lesson is also attended by Mrs. Ota, a 45-year-old widow and long-time mistress of his father, and her daughter Fumiko. Miss Kurimoto speaks disparagingly of Mrs. Ota, while at the same trying to awaken Kikuji's interest in Miss Inamura.
Kikuji and Mrs. Ota spend a passionate night together, and Kikuji wonders if Mrs. Ota sees his father in him. When she visits him again after a long pause, he learns that her daughter Fumiko tried to keep her from meeting him. Despite her deep sense of shame, she sleeps with Kikuji again. Late that night, Fumiko rings him to tell him that her mother committed suicide. He agrees to help Fumiko with covering up her mother's suicide to maintain her reputation.
Miss Kurimoto repeatedly shows up in Kikuji's house, speaking badly of Mrs. Ota while at the same time reminding him of Miss Inamura. Kikuji, annoyed by her intrusiveness, replies that he is not interested in the young woman. Fumiko bequests him a shino ware jar of her mother, and later a shino tea bowl, which allegedly bears an unremovable trace of her mother's lipstick. Kikuji develops an interest in Fumiko, asking himself if he sees her mother in her.
When Kikuji returns from a trip to Lake Nojiri, Miss Kurimoto brings him the news that both Miss Inamura and Fumiko have married another man in his absence. He learns that her story was a lie when Fumiko rings him to inform him that she will start a job and move into a flat farther away from him. Fumiko visits him later that evening and insists that her mother's tea bowl is of little value and should be destroyed. Kikuji places his father's tea bowl next to Mrs. Ota's, and they both are aware that these were the bowls his father and her mother drank from while they had their affair. Fumiko eventually shatters her mother's bowl on a stone plate. Later, Kikuji and Fumiko spend the night together.
The next day, Kikuji tries to ring Fumiko at her work, but she hasn't shown up. He goes to see her at her new flat, where he is told that she announced to go on a holiday with a friend. Kikuji speculates if Fumiko committed suicide like her mother.
