The relationship between gut microbiota and mitochondria is very close. On the one hand, intestinal microorganisms can directly or indirectly through the digestion of nutrients in food to produce metabolites such as short-chain fatty acids, hydrogen sulfide and nitric oxide, affect the energy metabolism process associated with mitochondria, regulate mitochondrial reactive oxygen species production, and regulate mitochondria and even the entire body's immune response. On the other hand, intestinal cell mitochondrial dysfunction and mitochondrial genome genetic variation also affect the composition and function of the gut microbiota. In this paper, we summarized recent advances in the relationship between gut microbiota and mitochondria. It provides a theoretical basis for targeting the intestinal flora and mitochondria to regulate intestinal health.