The invention provides an aquaculture water in-situ purification composite microbial membrane and a using method thereof, and belongs to the technical field of aquaculture and environmental protection. A functional element of the composite microbial membrane is a membrane component in which paenibacillus polymyxa, lactobacillus plantarum, rhodobacter sphaeroides, rhodococcus pyridinovorans, bacillus amyloliquefaciens and other beneficial microorganisms are immobilized. A preparation process of the aquaculture water in-situ purification composite microbial membrane comprises selecting of a soft packing microorganism carrier, composite bacteria liquid preparation, microorganism immobilization and other steps; the composite microbial membrane is mounted in aquaculture water, beneficial microbes begin activation reproduction, long-term regulation of microbial ecology of the aquaculture water can be realized, ammonia nitrogen, nitrite and hydrogen sulfide and other toxic and harmful substances in pond can be controlled, metabolites can be licked by farmed fish, shrimp, and other aquatic organisms, so that the immunity is improved, the growth speed of the farmed species is increased, and the aquaculture water in-situ purification composite microbial membrane is especially adapt to ponds for high density aquaculture of shrimp, crab, fish and the like.