Municipal saline organic wastewater inhibits microbial metabolic activities due to its low carbon-to-nitrogen (C/N) ratio and high salinity; thus hinders the removal of pollutants from the wastewater. Therefore, there is a great need for the technologies that can alleviate the inhibitory effects of salinity on biological processes. In this study, a sequencing batch reactor (SBR) was utilized, which was inoculated with municipal activated sludge and fed with synthetic wastewater of low C/N ratio and 1% salinity, provided only by solid NaCl. The analysis focused on the effects of halotolerant bacteria (for NH4+—N and TN reduction) on sludge characteristics, pollutant degradation performance, and microbial community changes during SBR operation. It was found that the presence of halotolerant bacteria promoted floc aggregation, increased sludge particle size, and enhanced protein (PN) content, which reached a maximum of 25.88 mg/L. Removal rates of 83.51% for COD, 81.96% for NH4+—N, 70.28% for TN, and 81.50% for TP were achieved by SBR. In the composition of bacterial communities, the dominant genera were Zoogloea, Flavobacterium,and norank_ f_norank_o_Saccharimonadales, whose synergistic effects were observed to enhance the system’s ability for nitrogen and phosphorus removal. Optimal conditions, as determined by response surface methodology, included an influent COD of 399.99 mg/L and a halotolerant bacteria dosage of 4.2 g. Under these conditions, the experimental mean removal rates for COD, NH4+—N, and TP were 82.31%, 90.75%, and 81.23%, respectively, which were close to the predicted values. These results indicated that the response surface prediction model performed well. These findings can offer valuable insights into the efficient treatment of saline wastewater by halotolerant activated sludge.