The main theme of Thousand Cranes is fate and the fact that, in this story at least, it seems to be inescapable. It was fate that brought protagonist Kikuji Mitani's father together with his varied mistresses because he enjoyed the idea of a traditional Japanese tea ceremony, and it was fate that brings Kikuji to yet another tea ceremony, where he meets the many women who will impact his life.

He falls for his father's former mistress, Mrs. Ota, who then commits suicide because of the guilt and shame their affair causes her. Then he falls again, perhaps even harder, for her daughter, but fate seems to have only heartache in store for them both. Just as the affair between his father and her mother was destined to end in tragedy, their love is doomed from the start. They cannot escape the sullied past that defines them, even when at the end of the story they shatter the glass bowl from a tea ceremony that symbolized their parents' relationship with each other.

It would have been very easy for Kikuji to fall, instead, for the charming and attractive Yukiko that his father's other mistress spends the entire novel trying to set him up with, but this isn't what fate wants. He is compelled to follow in his father's footsteps, no matter how much this hurts him.