The forward osmotic membrane bioreactor (FOMBR) is an emerging innovative technology with broad application prospects in the field of wastewater treatment. Its application is severely limited by concentration polarization, salinity accumulation, and evident water flux decline. Gradual salinity accumulation to a maximum conductivity of 19.7 mS cm under continuous flow operation suppressed the activities of sludge and biodegradation efficiencies. The employment of the regulation of intermittent supernatant discharge was first investigated to alleviate inhibition caused via accumulated salinity in the bioreactor, and bilateral influent was examined with respect to the performance of the FOMBR. The preferable condition to be applied was FO orientation mode (i.e. active layer facing feed) with spacers added to the surface. Given the decreased salt concentration with 2 L of the supernatant removed per day, the water flux declined more slowly and sludge activities were recovered. When compared to the performance without discharging supernatant, the strategy of controlling salinity could improve the removal efficiencies of NH-N, PO-P, and total organic carbon (TOC) by 15.1, 14.3, and 2.3%, respectively. Additionally, the sludge in the intermittent supernatant discharge bioreactor exhibited better sludge property, larger sludge particle size, and recovered sludge activities with the mixed liquid suspended solids (MLSS) stable at around 4.90 g L. Therefore, regulation of intermittent salt discharge and controlling the salinity concentration in bioreactor can be employed as an effective method to deal with concentration polarization and salinity accumulation in the FOMBR.