In recent decades, the incidences of metabolic syndrome of cultured fish caused by unbalanced nutrition components or excessively large energy intake, have dramatically increased globally, and triggered gut inflammation, metabolic disorders, body stress, and decreased immunity defense. Related studies have mainly focused on target tissues of the body, such as the liver and adipose tissue. However, intestinal microbiota in fish, as another most important "tissue", is usually neglected. The gut microbiota plays an important role in the process of growth and development, immune defense, energy absorption, and metabolism of lipids or glucose. To deeply address the relationship among the feed, gut microbes, and lipid metabolism in fish, we firstly clarified the main composition and structure of the gut microbiota in marine and fresh water fish. Then, the effects of feed lipid nutrition on intestinal microbes were analyzed, including the lipid source type and level. Regarding the relationship between the gut microbes and the body lipid metabolism, the causality and effects of the gut microbes on the lipid metabolism were expounded. Specifically, possible mechanisms of host lipid metabolism disorder because of altered gut microbes were described, focusing on the production of short chain fatty acids (SCFAs), lipopolysaccharide (LPS), bile acids, trimethylamine oxide (TMAO), and the permeation of the gut epithelial cells. In particular, several strategies regarding lipid metabolism regulation based on the microbes were advanced, such as the application of new feed sources, prebiotics, and probiotics. Thus, we suggested that the structure and compositional change of the gut microbiota could be used as the symbol for the dysfunction of host lipid metabolism. Furthermore, taking steps based on the theory of the gut steady-state will provide feasible ways to improve the lipid metabolism dysfunction of fish, including clarifying the interactive mechanisms between the microbes and the host, and exploring indigenous probiotics depending on the culture dependent methods and micro-ecological agents.