Abstract: To investigate the effects of synergistic bacteria-algae (Chlorella+ EM bacteria) on microbial community structures in the intestine and aquaculture water of Eriocheir sinensis cultured in photovoltaic-integrated ponds, three groups-photovoltaic (FPI), photovoltaic + synergistic bacteria-algae (FP-BA), and traditional pond (TAC)-underwent dynamic monitoring at 0, 30, 60 and 90 d. Results demonstrate that the FP-BA group significantly suppressed intestinal pathogenic Vibrio proliferation (reduced abundance vs. TAC at 90 d, P < 0.05), maintained probiotic Candidatus_Bacilloplasma dominance with minimal unique genera fluctuation, and enhanced microbial stability through replication and repair pathway enrichment; concurrently, FP-BA significantly increased abundances of water-purifying Planctomycetota and Pirellula (P < 0.05) with 30 d α-diversity surpassing FPI and TAC (P < 0.05). While TAC enriched more opportunistic pathogens (e.g., Vibrio, Enterobacter) and eutrophication indicators (e.g., Actinobacteriota), FPI exhibited reduced biodiversity, declined membrane transport function, and significantly higher cyanobacterial bloom risk (Microcystis) versus TAC at 90 d due to photovoltaic shading; conversely, FP-BA prioritized lipid metabolism and cofactor synthesis to mitigate organic pollution impacts. Synergistic bacteria-algae alleviated photovoltaic shading stress through dual pathways-intestinal probiotic maintenance and water purification, which can effectively circumvent risks in both traditional and photovoltaic aquaculture.