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The cultivation of largemouth bass (Micropterus salmoides), a species of significant economic value in aquaculture, has experienced notable growth recently. However, the deterioration of water quality seriously affects the metabolic responses of M. salmoides. While compound microbial agent (CMA) is widely utilized for ecological rehabilitation and water filtration, its application in M. salmoides has not been reported. Here, based on physio-biochemical tests and 16S rRNA sequencing, we investigated the effects of CMA (yeast, Bacillus subtilis, and lactic acid bacteria) on the water quality within the recirculating aquaculture system, along with physiological indices and gut microbiota of M. salmoides. Compared to the control and single microbial agent (yeast), CMA treatment improved the water quality by improving the dissolved oxygen and delaying the increase of pH, total nitrogen, total phosphorus, ammonia nitrogen, and nitrite. The 16s rRNA gene sequencing revealed that the water treated with CMA exhibited elevated levels of chao1, Shannon, Pd, and a larger population of dominant bacterial. Besides, higher values of ACE, chao1, Shannon, and OTU level, and lower Simpson index were found in CMA treated M. salmoides samples, suggesting that CMA treatment enhanced the species richness and diversity of gut microbiota of M. salmoides. Furthermore, CMA treatment hindered the generation and proliferation of harmful bacteria, such as the Mycoplasma mobile 163K species and the Erysipelotrichaceae family, which was associated with enhanced antioxidant enzymatic activity and decreased MDA level in both the serum and liver. These findings shed light on the essential roles of CMA in M. salmoides culturing and introduce an innovative approach to enhance the aquatic environment.