Biofloc technology (BFT) has been proven to perform closed, high-density aquaculture at a lower cost and has received much attention from aquaculturists in recent years. The two critical services of bioflocs in BFT aquaculture systems include removing ammonia nitrogen from feeding and providing nutrients for some cultured animals. The current experiment investigated the ammonia nitrogen removal efficiency and nutrient composition of bioflocs under the condition of two bioflocs concentrations (300 mg/L and 600 mg/L) and three Bacillus subtilis additions (104 CFU/mL, 105 CFU/mL and 106 CFU/mL) in the suspended growth reactors. The results showed that the bioflocs concentration had a significant effect (P < 0.05) on the removal rate of ammonia nitrogen. The highest ammonia nitrogen removal rate was (3.85 ± 0.27) mg N/h observed in the group with 600 mg/L bioflocs and 106 CFU/mL Bacillus subtilis, which was significantly higher than that in the 300 mg/L bioflocs groups. The bioflocs concentrations had a significant effect on the major nutrients (crude protein, crude ash, crude fat) and some amino acids in the bioflocs. There was no significant effect of bioflocs concentrations on the content of major nutrients (crude protein, crude ash, crude fat) and some amino acids in the bioflocs (P > 0.05). The crude protein content of the bioflocs was (27.22±0.47)% and (27.43±1.07)% for the 300 mg/L and 600 mg/L bioflocs groups with the Bacillus subtilis addition level of 106 CFU/mL, which was significantly higher than the other two bacteria addition levels. The copy numbers of four nitrification genes (ureC, amoA, nxrA, Hao) were higher in the groups at a concentration of 600 mg/L than in the 300 mg/L groups. The copy numbers of amoA, ureC and Hao genes in bioflocs increased with the addition of Bacillus subtilis. The results of the current study proved that the 600 mg/L bioflocs and 106 CFU/mL Bacillus subtilis were beneficial to improve the ammonia nitrogen removal rate and nutritional content of the bioflocs.