Intestinal flora coevolutes with the host and plays an important role in maintaining immune homeostasis. It participates in the development and progression of a variety of diseases, directly or indirectly through metabolites. Researchers have proposed the theories of the “gut-brain axis” and “gut-lung axis” based on the interrelationship between intestinal microecology and other organs. These theories have been widely verified in basic and clinical research fields. Long voyage personnel are prone to intestinal flora disorder and often suffer from other health problems. At present, studies should be actively carried out to clarify the relationship between intestinal flora disorder and health status of long voyage personnel and explore reasonable intervention measures to maintain intestinal microecological balance, improving the quality of life and preventing diseases among them.