Biofilters running steadily and efficiently are a crucial part in recirculating aquaculture system, but the operational process of biofilter may be affected by many environmental factors. In this paper, the influence of influent pH on nitrification performance of fluidized bed biofilter is studied in two parts: (1) the fluidized bed biofilter in the start-up stage of biofilm formation is studied, mainly focusing on the influence of influent pH (7.0, 7.5, 8.0, 8.5) on the starting of fluidized bed biofilter under the condition of natural biofilm formation. The results show that when pH is 7.5, the biofilter has the shortest starting time, and can run steadily after about 50 days and remove the most TAN and NO2—N. (2) After the biofilm is mature, specific to biofilter running steadily, the influence of pH (7.0, 7.5, 7.7, 8.0, 8.5) on nitrification performance of biofilter is studied. The results show that when pH is 7.7, the rate to remove TAN is the highest, reaching 0.58±0.020 mg/(L·h). In addition, when pH is 7.5, the effect to treat NO2—N is the best. It is also found in the test that there are different degrees of NO2—N accumulation in all treatment groups, which is intensified with increase of pH. Suitable influent pH can shorten the biofilm formation cycle and improve the nitrification performance of biofilter. The results can provide theoretical guidance for biofilm formation starting and stable running of seawater biofilter.