Engineer Jake Holman is a skilled mechanic who prefers to keep to himself and avoid getting involved in the politics and social hierarchy of the U.S.S. San Pablo. The gunboat is run by a captain who is more interested in maintaining the status quo and following orders than in truly connecting with the Chinese people they encounter along the river.
Holman becomes friendly with a local woman named Maily, who works at a nearby brothel. He also befriends a group of missionaries who run the China Light Mission. The missionaries are seeking to convert the local Chinese population to Christianity, but they face opposition and violence from rebels who resent foreign interference in their country.
As tensions between the Chinese and the gunboat crew increase, Holman finds himself caught in the middle. He realizes that he must take a stand and choose a side in the conflict, even if it means going against the orders of his superiors. In the end, Holman's actions have tragic consequences and change the course of his own life as well as those of the people he has come to know and care about. The Sand Pebbles explores themes of cultural clashes, imperialism, and the effects of war on individuals and societies.