The purpose of this study was to investigate the effects of increasing salinity on the performance and microbial community structure in a sequencing batch reactor (SBR) treating low C/N ratio wastewater. The SBR was subjected to a gradual increased salinity from 0 wt% to 3.0 wt% under low Chemical Oxygen Demand (COD)/N ratio, operating for 80 days. The study results indicated that high salinity decreased the removal efficiency of ammonium (NH-N) from 77.09% (1.0 wt%) to 45.7% (3.0wt%). The organic matter removal are not significantly affected by the high salinity. Non-metric Multi-Dimensional Scaling (NMDS) analysis showed that the gradual increased salinity altered the overall bacterial community structure, and low salinity (1wt%) promoted the bacterial diversity, while high salinity (2 wt% and 3 wt%) significantly decreased the bacterial diversity in low C/N ratio activated sludge system. Further analysis revealed that two genera related to nitrification process (unclassified- and g-) were inhibited, while a genus related to organic removal () and three genera related to denitrification (, and ) increased significantly at a salinity of 3 wt%. This study provides insights of shifts in the bacteria community under the stress of high salinity in low C/N ratio of activated sludge systems.