A primary theme in "The Ones Who Walk Away from Omelas" is morality. In an introduction to the story, Le Guin noted that it critiques American moral life. She explained the story's subtitle, "Variations on a Theme by William James," by mentioning that she was inspired by a concept James, an American psychologist and philosopher, discussed in "The Moral Philosopher and the Moral Life": "[If people could be] kept permanently happy on the one simple condition that a certain lost soul on the far-off edge of things should lead a life of lonely torment, ... how hideous a thing would be [the enjoyment of this happiness] when deliberately accepted as the fruit of such a bargain." While James believed people would refuse such an agreement, Le Guin depicts in "The Ones Who Walk Away from Omelas" a community that accepts it, allowing her to explore why people avoid or abandon moral responsibility. Interestingly, those who decide to leave Omelas after witnessing the child's plight are scarcely noticed, and their rebellious act is neither comprehended by the citizens nor the storyteller.

As a political allegory, in which characters represent concepts or ideas to convey a political message, "The Ones Who Walk Away from Omelas" also examines the morality behind political systems. The child is frequently interpreted as a symbol of the underprivileged in capitalist Western societies, especially the United States, as well as the destitute countries of the Third World. In both contexts, the disadvantaged and impoverished are often exploited and disregarded by the wealthy and successful. Thus, Le Guin explores the moral responsibility of a society where the happiness of the majority is built on the suffering of a powerless minority.

Additionally, Le Guin examines the moral obligation of writers and readers by crafting a narrative where the narrator encourages the reader to participate in the creation of Omelas. As the reader is invited to imagine Omelas "as your fancy bids," they are subtly led to accept Omelas and the grim foundation on which it is built. As a result, the reader, much like the citizens of Omelas, is confronted with a choice: to either embrace the society or reject it on the basis of moral indignation.