Pseudomonas stutzeri XL-2, with the capability of heterotrophic nitrification-aerobic denitrification and biofilm-forming, was applied in a sequencing batch biofilm reactor (SBBR) for bioaugmented treatment of ammonium-rich wastewater. The bioaugmented system SBBR 1 showed a rapid development of biofilm and relatively shorter time for biofilm hanging compared with the control system SBBR 2 without strain XL-2 inoculation. At different NH4+-N loads of 100, 200 and 300 mg/L, the effluent TN removal ratios ranged in 88.7–97.0%, 85.1–93.5% and 87.8–92.5% respectively in SBBR 1, while only ranged in 77.4–85.4%, 77.1–84.3% and 79.8–85.0% in SBBR 2. Less accumulation of NO2−-N and NO3−-N resulted in the better performance on TN removal in SBBR 1. Microbial community structure analysis revealed that strain XL-2 successfully proliferated in SBBR 1 and contributed to the less accumulation of NO2−-N and NO3−-N as well as biofilm formation.