The original Japanese edition was released in three parts, which make up the three "books" of the single volume English language version.

In English translation, two chapters were originally published in The New Yorker under the titles "The Zoo Attack" on July 31, 1995, and "Another Way to Die" on January 20, 1997.

A slightly different version of the first chapter translated by Alfred Birnbaum was published in the collection The Elephant Vanishes under the title "The Wind-up Bird and Tuesday's Women".

[1] The first part, "The Thieving Magpie", begins with the narrator, Toru Okada, a low-key and unemployed lawyer's assistant, being tasked by his wife, Kumiko, to find their missing cat.

Kumiko's family believes in fortune-telling and had previously stipulated that the couple meet with an elderly man, Mr. Honda, for consultations on a regular basis, which they did for some time.

(Instead of giving advice, he spends most of their sessions retelling the same story of his experience in the Kwantung Army in the lost tank battle with the Russians at Nomonhan on the Manchukuo-Russian border during World War II.)

Creta meets Toru at his home and begins to tell him the story of her past, involving being raped by Noboru, but abruptly leaves.

The first section ends with Lieutenant Mamiya arriving and telling Toru a long tale about his eerie and mystical wartime experiences in Manchukuo in the Kwantung Army, where he sees a man skinned alive.

Confused, Toru tries several things to calm himself and think through the situation: talking and taking up work with May Kasahara, hiding at the bottom of the well, and loitering around the city looking at people.

While at the bottom of the well (of the abandoned house), Toru reminisces about earlier times with Kumiko, including their first date to an aquarium where they looked at jellyfish.

He also experiences a dreamlike sequence where he enters a hotel room and speaks with a woman, and notices a strange blue mark on his cheek after he leaves the well.

In return, Toru receives pay and partial possession of the abandoned house that had been purchased to resell by some property agency.

Cinnamon, Nutmeg's son, maintains the house and refits the well with a ladder and pulley to open and close the well cap from the bottom.

Toru discusses Kumiko's disappearance with Noboru directly and indirectly (through his agent Ushikawa) and eventually arranges for a talk with her through the Internet, using her recollection of the jellyfish date as a means to verify her identity.

Kumiko sends him a message on the computer to let him know she is alright but intends to kill Noboru by pulling the plug on the life support.

[16] Kirkus Reviews wrote that the novel was "a major work bringing signature themes of alienation, dislocation, and nameless fears through the saga of a gentle man forced to trade the familiar for the utterly unknown" and "a fully mature, engrossing tale of individual and national destinies entwined" that would be "hard to surpass.

"[17] Michiko Kakutani, in The New York Times, regarded the novel as "a wildly ambitious book that not only recapitulates the themes, motifs and preoccupations of his earlier work, but also aspires to invest that material with weighty mythic and historical significance" though was "only intermittently successful."

While she finds that the novel succeeds in articulating that the world is "a mysterious place", that same confusion also "seems so messy that its refusal of closure feels less like an artistic choice than simple laziness".

[18] Many regard The Wind-Up Bird Chronicle as Murakami's masterpiece, and it appeared in The Telegraph's 2014 list of the 10 all-time greatest Asian novels.