In order to improve the performance of microbial fuel cell (MFC), PVA/PWA and PVA/OPD modified membranes were prepared by solution impregnation with polyvinyl alcohol (PVA) as adhesive and phosphotungstic acid (PWA) and o-phenylenediamine (OPD) as modifier respectively, and the modified membranes were mounted on MFC system. The membrane properties were characterized by SEM, EIS, CV and water absorption, the effects of membrane modification on the output power and the removal rate of chemical oxygen demand (COD) of MFC were investigated. Results showed that both PVA/PWA and PVA/OPD modified membranes could improve the performance of MFC to a certain extent, but PVA/OPD modified membrane presented a better effect. The water absorption of PVA/OPD modified membrane was about 14.49%, which was 122.9% higher than that of the conventional Nafion membrane (NF). The output energy of MFC with PVA/OPD modified membrane in the test cycle was 101.75 J, which was 587.5% higher than that of MFC with NF; the COD removal rate of amoxicillin pharmaceutical wastewater was 66.2%, which was 48.7% higher than that of MFC with NF. The membrane modification method based on PVA/OPD has a significant effect on improving the power generation performance and wastewater treatment efficiency of MFCs.