Three pilot sequencing batch reactors (SBRs) were employed to treat aquaculture wastewater from a recirculating aquaculture system (RAS) stocking GIFT Oreochromis niloticus using biofloc technology (BFT), under three designed MLSS (1 500 mg/L, 3 000 mg/L, 5 000 mg/L). The results showed that, the effluent concentrations of ammonia (TAN), nitrate (NO₂^--N) and nitrate (NO₃^--N) in SBRs were (0.29-0.39) mg/L, (0.005-0.006) mg/L, and (7.11-7.60) mg/L, respectively; these average removal rates were 82.20%-86.20%, 98.40%, and 38.40%-40.00%, respectively (P>0.05); the volume removal loads were (2.51-2.64) g/(m³·d), (0.56±0.08) g/(m³·d), and (8.52-9.78) g/(m³·d); meanwhile, the removal rates and volume removal loads of solubility inorganic nitrogen (DIN) were 43.20%-44.60%, (10.25-11.61) g/(m³·d). However, the protein contents of flocs from SBRs showed no significant differences among the three groups, as 30.00%±1.32%, 29.87%±0.67%, and 31.00%±0.75%, respectively. The crude lipid contents were detected at 9.51%±0.94%, 4.37%±0.42%, and 3.65%±0.22%, and the crude ash content in 1 500 mg/L group is significantly higher than those in the other two groups (P<0.05). Besides, analysis of high-throughput sequencing revealed that Proteobacteria accounted for the most phyla of bioflocs in SBRs (44.66%, 44.51%, 44.29%), followed by Bacteroidetes (13.89%, 13.98%, 14.07%); at the genus levels, Alishewanella, Blastocatella, Amaricoccus, Rhodobacteraceae_unclassified, Terrimonas and Devosia were identified to be the dominant genera. All the results suggest that the pilot SBRs have good effects on nitrogen removal, and will contribute to realizing the resource utilization of aquaculture wastewater.