Start-up of membrane bioreactor under different NaCl stress was investigated in this study. Results showed that nearly 90% chemical oxygen demands and ammonia nitrogen ([Formula: see text]-N) was oxidized in none and 0.5% NaCl condition during the start-up stage. While 1% NaCl dramatically depressed the utilization of [Formula: see text]-N and about 4 weeks were required for adaption of sludge biomass to saline condition. In addition, the accumulation of nitrite high to 11.84 mg/L was observed in 1% NaCl stress, indicating the more inhibition on the activity of nitrite oxidizing bacteria. Microbial community responded to the different salinity levels. The phylum Proteobacteria and Bacteroidetes occupied over 60% in all the three MBRs. Salinity enriched the relative abundance of Maribacter, Methyloversatilis, Aeromonas and Curvibacter, while reducing the proportion of Nitrospira and Haliscomenobacter. Nitrospirae decreased sharply at 1% NaCl accounting for the accumulation of nitrite. Higher content of soluble microbial products (SMP) under saliferous MBR were released, which deteriorated the permeability of membrane module. Protein-like substances and humic substances were the main ingredients of SMP, of which the former contributed more to membrane flux decline. This study provided better understanding on the impact of salinity on the start-up of MBR.