Abstract Application of traditional bait in freshwater aquaculture caused environment pollution and disease frequent occurrence. Effluent after Rubrivivax gelatinosus ATCC 49846 (R. gelatinosus) wastewater treatment could be re-utilized to culture Crucian carp as microbial feeds and aquaculture water. Therefore, a novel integrated system of wastewater treatment, the improvement of yield, digestion system, intestinal microbiota and aquaculture water quality of Crucian carp by effluent containing R. gelatinosus was proposed and investigated. Crucian carp could grow well in the effluent containing immobilized cells of R. gelatinosus ATCC 49846 in sodium alginate (ER) group. Survival rate and yield under ER group were almost same with control group (CK). The whole fish body composition under ER group were increased compared with CK. Biochemicals and remainder substances in effluent and R. gelatinosus enhanced protease, amylase, lipase activities. Theoretical analysis showed biochemical substances regulated these enzyme activities as component, active center. Moreover, R. gelatinosus and biochemical substances improved intestinal microbiota, the growth of intestinal probiotics and ATP production. Meanwhile, R. gelatinosus in effluent also purified aquaculture water quality. This technology would saved the water of aquaculture, reduced the water pollution and wastewater discharge, and improved the output, digestion system and intestinal microbiota of Crucian carp simultaneously.