Aquaculture, as one of the largest food production sectors, is a candidate industry to solve the worldwide food shortage. Nitrogenous compounds from uneaten feed and excretion continually destroy the rearing water quality during the breeding which causes slow growth, production reduction, and even death. Thus, alleviating water contamination can improve fish welfare and prevent disease occurrence. In the present study, a stable bacteria-microalgae association was used to construct a biofortified crucian carps culture system without water exchange. During the 8-week experiments, the water quality, fish production, and intestinal health were assessed. In this biofortified system, water quality was significantly improved and the content of total ammonia-N and nitrite-N was finally in a state of dynamic equilibrium at a lower concentration compared with that in blank control. The final body weight of crucian carps in the bacteria-microalgae groups was significantly improved by 10.52%. The crucian carps intestinal health including amylase and lipase activities, villus length and width, and muscle thickness was also significantly increased by 56.33%, 63.89%, 347.25%, 98.48%, and 129.53%, respectively, in bacteria-microalgae groups. Intestinal microbiota was improved significantly by changing the microbiota composition and LEfSe analysis demonstrated that some genera frequently found in the intestines of stressed and dying animals were enriched in crucian carps intestine in blank control. The KEGG prediction proved that metabolisms including carbon metabolism, pyruvate metabolism, and fatty acid metabolism were significantly improved. In summary, the bacteria-microalgae association biofortified culture system improved the rearing water quality, and then improved the intestinal health of crucian carp, eventually increased the production of crucian carp.