To improve the efficiency of simultaneous heterotrophic nitrification and aerobic denitrification (SND) at high concentrations of NaCl and ammonia nitrogen (NH4+—N), we investigated the SND characteristics of Halomonas bacteria with the ability to synthesize the compatible solute ectoine. Halomonas sp. strain B01, which was isolated, screened and identified in this study, could simultaneously remove nitrogen (N) by SND and synthesize ectoine under high NaCl conditions. Gene cloning and sequencing analysis indicated that this bacterial genome contains ammonia monooxygenase (amoA) and nitrate reductase (narH) genes. Optimal conditions for N removal in a solution containing 600 mg/L NH4+–N were as follows: sodium succinate supplied as organic carbon (C) source at a C/N ratio of 5, pH 8 and shaking culture at 90 rpm. The N removal rate was 96.0% under these conditions. The SND by Halomonas sp. strain B01 was performed in N removal medium containing 60 g/L NaCl and 4,000 mg/L NH4+–N; after 180 h the residual total inorganic N concentration was 21.7 mg/L and the N removal rate was 99.2%. Halomonas sp. strain B01, with the ability to synthesize the compatible solute ectoine, could simultaneously tolerate high concentrations of NaCl and NH4+–N and efficiently perform N removal by SND.