The effects of salinity on the activity in nutrient removal, settling and microbial community of activated sludge in sequencing batch reactors (SBRs) treating synthetic saline wastewater were investigated. Two SBRs, one treating synthetic saline wastewater (the N-Reactor, with NaCl addition) and the other treating fresh synthetic wastewater (the C-Reactor, without NaCl addition), were operated for 68 days. Three salinities (in terms of concentrations of NaCl)—10, 20 and 40 g NaCl/l—were examined. The microbial activity described with the specific glucose utilization rate, specific nitritation and nitratation rates, and specific phosphorus release and uptake rates, was inhibited in the N-Reactor, in comparison with that in the C-Reactor, except that the specific nitritation and nitratation rates were improved at the salinity of 10 g NaCl/l. The sludge yield coefficient decreased at salinities of 10 and 20 g NaCl/l but it rose at the salinity of 40 g NaCl/l. The settling of activated sludge flocs, in terms of the sludge volume index (SVI), was improved by adding NaCl. Particularly in the first 5 minutes during the SVI measurement, activated sludge flocs in the N-Reactor settled much faster than those in the C-Reactor. However, the effluent from the N-Reactor contained higher suspended solids than the effluent from the C-Reactor. The microbial diversity decreased with increasing the salinity, and the microbial community structure was greatly influenced by the salinity. Bacteriodetes and Actinobacteria were the dominant phylums detected with molecular fingerprinting techniques.