<p>The mammalian gut harbors an immensely diverse and abundant community of microorganisms that continuously interact with the host throughout life, shaping the host's immune system and influencing the development and progression of various immune-related diseases. Gut microbiota exert their effects on the host immune system through metabolites such as secondary bile acids, short-chain fatty acids, and tryptophan derivatives. These effects are not confined to the gut; metabolites can enter the circulatory system, or gut immune cells can migrate, thereby influencing the immune microenvironment throughout the body and the development of related diseases. This review discusses the types and production pathways of microbial metabolites that can directly impact the host immune system, and how these metabolites influence related diseases by affecting specific immune cells.</p>