The aim of this paper is to investigate the effects of inner-pond raceway aquaculture (IPRA) on the growth performance, antioxidant enzymes, digestive enzymes, digestive tract structure, and bacterial flora of Micropterus salmoides. There were four tanks in a pond with a recirculating flowing water culture, two of them were set up as the treatment group with flowing water, and the other two were set up as the control group with still water. The experiment lasted for 153 days. Relevant growth, biochemical indicators, and histomorphological structures were measured at the midway and the end of the culture period, and the microorganisms in the digestive tract were analyzed using the Illumina Miseq sequencing platform. Results showed that, ① Halfway through the culture period, the weight gain rate, specific growth rate, and condition factor of the treated group were lower than those of the control group. At the end of the culture period, the weight gain rate, specific growth rate, and condition factor of the treated group continued to decrease, although the treatment group’s survival rate was always higher than that of the control group. ② Halfway through the culture period, liver SOD and CAT in the treated group were significantly higher than those in the control group. MDA (0.16±0.01, 0.14±0.01 μmol/mg) in the treatment group was significantly lower than that in the control group (0.19±0.02, 0.21±0.02 μmol/mg), while digestive enzyme activity in the treatment group was significantly higher than that in the control group. By the end of the culture, antioxidant enzymes and digestive enzyme activity were declining to some extent, while SOD (55.11±3.91, 58.18±4.52 μmol/mg) in the treated group were still obviously higher than those (46.57±3.41, 48.84±3.62 μmol/mg) in the control group. ③ The height and density of intestinal villus in the treated group were significantly higher than those in the control group, and more digestive enzymes were secreted midway through the culture, which strengthened the digestive and absorptive functions of the intestine. ④ Halfway through the culture, there was a significant increase in the species diversity and evenness of the gastrointestinal flora of the M. salmoides in flowing water. However, by the end of the culture, the gastrointestinal diversity and evenness indices of the treated group were decreasing. In addition, midway through the culture, the stomachs of the treated group and the control group contained Helotiales and Cyanobacteria. The dominant bacteria found in the stomachs of the threatment group and control group were Proteobacteria and Firmicutes respectively, while the dominant bacteria found in the intestines of the control group were Firmicutes and then Proteobacteria. Towards the later stages of culture, the dominant bacteria found in the stomachs and intestines of both the treatment group and control group were Helotiales, while the dominant bacteria present in the culture water were Proteobacteria and Actinobacteria. The present study shows that continuous movement of water under IPRA can reduce the growth indexes.