The two ambient forward osmosis membrane bioreactors (M-FOMBR and A-FOMBR) with same operating condition were utilized to treat the effluent of mesophilic and ambient anaerobic bioreactors, respectively. It could be observed that the FOMBR could significantly remove the NH4+-N, PO43−-P and total organic carbon (TOC) in the influent, and the removals of NH4+-N, PO43−-P and TOC were related to the microorganism community. With operation time, the flux decline of M-FOMBR was gradually higher than that of A-FOMBR. The higher content of SMP may be one of the reasons for severe membrane fouling in the M-FOMBR, and the different soluble microbial products (SMP) content between the M-FOMBR and A-FOMBR might be associated with the variation of microbial community structures. The microbial community analysis showed that the abundance of Bacteroidetes in the M-FOMBR cake sludge was much higher than that in the A-FOMBR cake sludge. For the Bacteroidetes phylum, the most abundant bacterial genus was Chryseolinea. Therefore, the decrease of Chryseolinea in cake sludge might be responsible for membrane fouling mitigation.