The ectopic biofloc reactor was used to compare the simulated carbon sources (NaHCO₃) concentration of 0.0 g/L (control group), 0.5 g/L, 1.0 g/L and 1.5 g/L of simulated aquaculture wastewater which affected the nitrogen reduction and sedimentation performance of the bioflocs in two stages: organic carbon source existed (stage I for 21 d) and organic carbon source was missing (stage II for 21 d). The results showed that the effluent ammonia nitrogen concentration in the first-stage control group was significantly higher than that in the other treatment groups (P < 0.05), but generally decreased first and then stabilized. The nitrite nitrogen and nitrate nitrogen in each group accumulated a small amount; the biofloc biomass and sedimentation rate of the control group were significantly lower than the treatment groups (P < 0.05), and the difference between the treatment groups was not significant. There was no significant difference in the concentration of ammonia nitrogen and nitrite nitrogen in the effluent of each group in stage II (P > 0.05). The concentration of nitrate nitrogen in the control group was higher than that in treatment groups, and the concentration of ammonia nitrogen decreased rapidly. At this stage, the biomass and sedimentation rate of the bioflocs decreased, and the 1.0 g/L NaHCO₃ treatment group showed better sedimentation effect; the particle size distribution also tends to be uniform. During the whole experimental period, the removal efficiency of ammonia nitrogen reached 97.8% and the nitrite nitrogen did not accumulate significantly at different concentrations of inorganic carbon source. The sedimentation rate and biomass of bioflocs in the treatment groups were significantly higher than those in the control group (P < 0.05). The results show that the addition of inorganic carbon source can improve the nitrogen reduction performance of bioflocs and enhance its sedimentation rate. After removing the organic carbon source, the biofloc reactor can maintain the ammonia nitrogen removal capacity, but caused nitrate nitrogen accumulation, and reduction of biofloc organisms. When the organic carbon source was missing, the inorganic carbon source (≥0.5 g/L) could help the biofloc reactor to maintain its ammonia nitrogen removal capacity.