Oxidative decomposition of carbohydrate is an important source of energy for fish. Since carbohydrates are relatively cheap, adding appropriate amounts of carbohydrates to the feed can save protein, reduce feed costs, and reduce ammonia nitrogen excretion. However, a large number of studies have shown that fish have low ability to utilize carbohydrate. When carbohydrates content in the feed exceeds a certain level, the fish will suffer from impaired disease resistance, growth retardation, fatty liver, and higher mortality. Gut microbiota participates in the metabolism of various nutrients such as carbohydrates, lipids and amino acids, which significantly affects the animal nutritional metabolic processes. Increasing the utilization rate of feed has important practical significance for increasing fish production and farmers’ income. This review starts from the carbohydrate metabolism of fish and targets the microbial flora of fish digestive tract. Further, it explains the ways and possible mechanisms associated with the regulation of fish carbohydrate metabolism by gut microbiota. This review may provide new perspectives for efficient carbohydrates usage and protein saving in fish culture.