In order to improve the wastewater treatment effect and power generation performance of microbial fuel cell (MFC), a kind of carbon felt (CF) anode modified by sodium alginate and polyquaternium 11 (SA-PQ-11/CF) was prepared. A microbial fuel cell (MFC) experimental system was constructed using pharmaceutical wastewater and molasses wastewater as anode solutions and carbon felt as cathode, respectively, and its performance was characterized by scanning electron microscope (SEM), electrochemical impedance spectroscopy (EIS), cyclic voltammetry (CV) and chemical oxygen demand (COD). The results showed that the SA-PQ-11/CF anode had a larger specific surface area, and the solution resistance and charge transfer resistance of MFC were also significantly reduced. When the anolyte was pharmaceutical wastewater, the steady-state output voltage and the COD removal rate of MFC using SA-PQ-11/CF anode were about 0.22 V and 62%, respectively, which were 100% and 130% higher than those using CF. When the anolyte was molasses wastewater, the steady-state voltage and COD of MFC using SA-PQ-11/CF anode were 0.15 V and 43%, respectively, which were 275% and 95% higher than those using CF anode. The anode modification based on SA-PQ-11 can effectively improve the wastewater treatment efficiency and power generation capacity of MFC.