This study focused on the secretion of extracellular polymeric substances (EPSs), reactor nutrient removal performance and the microbial community under varying concentrations of NaCl (0, 10, 20, 30 and 40 g/L) during a granulation process in a sequencing batch reactor (SBR). The microorganisms tended to secrete higher levels of protein (PN) and polysaccharide (PS) as a protective mechanism under saline conditions, with tightly bound EPS (TB-EPS) playing a crucial role in stabilizing granules. An overall high removal rate of chemical oxygen demand (COD) throughout operation was observed. However, the removal rate of total nitrogen (TN) progressively decreased with the stepwise increase in salinity from 85.59% at 10 g/L to 64.18% at 40 g/L. The low total phosphorus (TP) removal efficiency during the operation process is due to the loss of sludge biomass and inhibition of phosphorus-accumulating bacteria activity. Moreover, salinity caused the changes in microbial community structure. Paracoccus, Thauera and unclassified_f_Rhodobacteraceae were dominant genera at 10 g, 20 g/L and 30 g/L salinity, respectively, while Azoarcus, Halomonas, unclassified_f_Flavobacteriaceaeand Vibrio replaced them at 40 g/L salinity.