Gut microbiota is important and plays a crucial role in the host health and nutritional metabolism through multiple mechanisms. Short‐chain fatty acids (SCFAs), which are carboxylic acids with aliphatic tails < 6 carbons, are mainly produced by anaerobic microbiota through fermentation of carbohydrates in the intestine. Acetate, propionate and butyrate are the most abundant SCFAs metabolites, important in energy homoeostasis, metabolism and the maintenance of gut health. In this review, we describe and document what is known about the production, absorption, transport and receptors as well as the factors that affect SCFA production in aquatic animals. Some evidence on the roles that SCFAs as feed additives play in improving growth performance, digestibility, survival rate, immune responses, disease resistance and structure and function of the intestinal tract and abundance of commensal microbiota in aquatic animals is summarized. In addition, the immune regulatory mechanism of SCFAs is highlighted. Although the effects of SCFAs in aquatic animals have been explored, further research is needed to profoundly investigate the mechanisms that by which SCFAs induce their effects on host metabolism.