The invention provides a method for treating aquaculture sewage based on microbial degradation, and belongs to the technical field of environmental protection. According to the method, a filtering filler loaded with algae bacteria is provided for preliminary adsorption and filtration of sewage, and algae bacteria fixed pellets are provided for symbiotic purification of the sewage. The algae bacteria are placed in a nitrogen-free phosphorus-free culture environment for enlargement culture, and nitrogen and phosphorus domestication is performed before loading or fixing, when the domestication operation is terminated, a weight percentage of ammonia nitrogen in the culture environment is at least 25%, and a weight percentage of phosphorus is at least 20%. The method has remarkable decontamination and deodorization treatment effects, can adapt to large changes in the nitrogen and phosphorus content of sewage, and treatment temperature, has high microbial nitrogen and phosphorus tolerance and removal rate, and has low treatment input cost and energy consumption. The used filtering filler has large loading capacity, high adsorption capacity and adsorption efficiency, and low biological loss during a storage period. The used algal bacteria fixed pellets have high mass transfer efficiency, good anti-microbial decomposition performance, long storage period and effective use period, and high sewage treatment efficiency of the microorganism at a relatively low temperature.