In order to improve the efficiency and reduce the cost of marine aquaculture circulating water treatment, the combined process of biological aerated filter and electrochemical oxidation was developed in this study. The removal efficiencies of ammonia and nitrite at different anode potentials, influent ammonia and nitrite concentration were investigated. The interaction between microorganisms and the anode was studied and the energy consumption of electrochemical reaction was analyzed. When the hydraulic detention time is 45 min, at the anode potential of 1.4 V, and the ammonia and nitrite concentration is respectively 4.5 and 1.3 mg/L, the removal rate of ammonia by biological-electrooxidation system reached 88.8%, which was 7.6% higher than that of the control group. The concentration of ammonia and nitrite in effluent is respectively 0.5 and 0.9 mg/L, the removal rate of COD is 88.2%, which was 19.4% higher than the control group. The average energy consumption of electrochemical reaction is 0.040 kWh/m³. Microbial growth on electrode surface can promote the anodic oxidation process. The results of microbial function prediction show that the proportion of nitrification function is 0.03% in the experimental group and 0.07% in the control group. In conclusion, the biological-electrooxidation method shows good performance of removing pollutants in the marine aquaculture circulating water and great potential for developing high efficient marine aquaculture recirculating water treatment.