A novel aerobic denitrifying bacterium Bacillus cereus J1 was isolated from a sewage treatment plant. Its characteristics under two distinct nitrogen sources were systematically investigated. According to the results of whole-genome sequencing, we inferred that strain J1 removes nitrogen through processes such as aerobic denitrification, dissimilatory nitrate reduction to ammonium, and ammonium assimilation. The degradation process of COD and total inorganic nitrogen (TIN) correlated to the zero-order degradation kinetics equation, and the maximum removal rate of NO3−−N reached 3.17 mg/L/h and that of NH4+−N was 3.79 mg/L/h. Utilizing single-factor experiments and response surface methodology, the optimal conditions for nitrate removal were determined as a shaking speed of 115 rpm, COD/nitrogen mass (C/N ratio) of 12.25, and salinity of 3.44 g/L, with the C/N ratio exerting the most significant influence. Similarly, for the maximum ammonium removal, the ideal conditions involved a shaking speed of 133 rpm, C/N ratio of 29, and salinity of 13.30 g/L, with the shaking speed exerting the most significant influence. These findings demonstrate that large amounts of ammonium and nitrate can be quickly removed with the help of Bacillus cereus J1, indicating that strain J1 may be applied to alleviate nitrogen pollution in aquatic environments.