Sodium dodecylbenzene sulfonate (SDBS) and sodium dodecyl sulfate (SDS), as two anionic surfactants, have diffused into environments such as surface water and ground water due to extensive and improper use. The effects on the removal performance and microbial community of sequencing batch reactors (SBRs) need to be investigated in the treatment of saline wastewater containing 20 g/L NaCl. The presence of SDS and SDBS could decrease the removal efficiencies of ammonia nitrogen and total phosphorus, and the effect of SDS was more significant. The effect of surfactants on the removal mainly occurred during the aeration phase. Adding SDS and SDBS can reduce the content of extracellular polymeric substances (EPS). In addition, SDS and SDBS also can reduce the inhibition of high salinity on sludge activity. A total of 16 s of rRNA sequencing analysis showed that the addition of surfactants reduced the diversity of microbial communities; besides, the relative abundance value of the dominant population Proteobacteria increased from 91.66% to 97.12% and 93.48% when SDS and SDBS were added into the system, respectively.