A system for treating wastewater containing organic compounds is provided, comprising an anaerobic bioreactor, an aerobic bioreactor disposed rearwardly of the anaerobic bioreactor, and a membrane separation reactor disposed rearwardly of the aerobic bioreactor. The system is capable of removing organic pollutants in wastewater through biological treatment process and separating solid from the liquid ones by using a membrane. By employing the system for treating wastewater containing organic pollutants, organic pollutants can be effectively eliminated and the problem of scaling and fouling on the surface of the membrane prevented, thus achieving the objectives of lowering cost and improving efficiency.