The effect of aerobic/anoxic duration on the performance, microbial community and enzymatic activity of sequencing batch biofilm reactor (SBBR) were investigated in treating mariculture wastewater. The microbial oxygen uptake rate and nitrifying rate gradually decreased with the aerobic/anoxic duration from 120/210 to 30/300min, whereas the nitrite reducing rate and nitrate reducing rate had the opposite results. The activities of dehydrogenase, ammonia monooxygenase and nitrite oxidoreductase gradually decreased with the aerobic/anoxic duration from 120/210 to 30/300min, but the activities of nitrate reductase and nitrite reductase had a gradual increment. The microbial nitrogen removal rates had similar changing trends to their corresponding enzymatic activities at different aerobic/anoxic duration. The variation of aerobic/anoxic duration obviously affected the microbial richness and diversity of SBBR. The co-occurrence, keystone taxa and significant difference of microbial community had some changes with the aerobic/anoxic duration from 120/210 to 30/300min.