This study would investigate the effect of nano-Fe₃O₄ particles on the performance of membrane bioreactor (MBR), including membrane fouling, membrane rejection and microbial community. It can effectively alleviate membrane fouling and improve the effluent quality in MBR by bio-effect rather than nanoparticle adsorption. The lowest membrane fouling resistance was achieved at R_4-MBR (sludge and membrane surface with nano-Fe₃O₄), which decreased by 46.08%. Meanwhile, R_3-MBR (sludge with nano-Fe₃O₄) had the lowest concentration of COD in effluent which was below 20 mg/L in the stable phase of MBR operation. After applying nano-Fe₃O₄, the content of extracellular polymeric substances (EPS) and soluble microbial products (SMP) were both reduced with a lower molecular weight. From the microbial community analysis, the abundance of Proteobacteria increased from 25.06 to 45.11% at the phylum level in R_3-MBR. It contributed to removing organic substances in MBRs. Moreover, the nano-Fe₃O₄ restricted Bacteroidetes growth, especially in R_4-MBR, leading to a more excellent performance of membrane flux. Besides, the applied nano-Fe₃O₄ promoted the abundance of Quorum Quenching (QQ) microorganism, and declined the percentage of Quorum Sensing (QS) bacteria. Then, a lower content of N-Acyl-_l-Homoserine Lactones (AHLs) in containing nano-Fe₃O₄ sludge. That was also prone to control membrane fouling. Overall, this study indicates the nano-Fe₃O₄ particle is appropriate for elevating MBR performance, such as membrane fouling and effluent quality, by bio-effect.