The microbial fuel cell (MFC) has emerged as a promising technology for wastewater treatment and energy recovery, but the expensive cost of proton exchange membranes (PEMs) is a problem that need to be solved. In this study, a two-chamber MFC based on our self-made PEM sulfonated poly (ether ether ketone) membrane was set up to treat phenol/acetone wastewater and synchronously generate power. The maximum output voltage was 240-250 mV. Using phenol and acetone as substrates, the power generation time in an operation cycle was 289 h. The MFC exhibited good removal performance, with no phenol or acetone detected, respectively, when the phenol concentration was lower than 50 mg/L and the acetone concentration was lower than 100 mg/L. This study provides a cheap and eco-friendly way to treat phenol/acetone wastewater and generate useful energy by MFC technology.