The effects of salinity on the performance and microbial community structure of activated sludge were investigated in an anoxic-aerobic sequencing batch reactor (SBR). The removal efficiencies of chemical oxygen demand (COD) and -N decreased as the influent salinity increased from 0.5% to 6%. The specific oxygen utilization rate of activated sludge increased from 22.47 to 43.16 mg O2 g−1 mixed liquid suspended solids (MLSS) h−1 with the increase in salinity from 0.5% to 4% and subsequently decreased to 18.3 mg O2 g−1 MLSS h−1 at 6% salinity. The specific ammonium oxidation rate (SAOR) and specific nitrite oxidation rate (SNOR) decreased slowly at 0.5–1% salinity and then decreased rapidly with the increase in salinity from 1% to 6%. The SNOR diminished at a faster rate than the SAOR with the increase in salinity from 0.5% to 6%. The specific nitrate reduction rate (SNRR) decreased with the increase in salinity, whereas the SNRR was higher than the sum of SAOR and SNOR at 0.5–6% salinity. The denaturing gradient gel electrophoresis profiles revealed obvious changes in microbial community structure at different salinities. Some microbes were capable of tolerating up to 6% salinity in the SBR, such as Planomonospora sphaerica, Nitrosomonas sp. Is32, and Denitromonas sp. D2–1.