The treatment of wastewater by microalgae cultivation has attracted more and more attention. However, the way to harvest microalgae cells from the wastewater and the treatment of the large quantity of residual solution have become critical issues. In this work, a new approach for the treatment of municipal wastewater is presented. The combination of flocculation for removing mainly microalgae and thereafter membrane filtration for chemical oxygen demand (COD) and conductivity reduction of the residual solution after flocculation is discussed. The COD concentration of the wastewater decreased from 260 to 84 mg/L after flocculation by chitosan. Five ultrafiltration (UF) membranes and two nanofiltration (NF) membranes were used for filtration to find a suitable membrane for COD and conductivity reduction. Among the five UF membranes, GR82PE showed the best performance, whose permeate flux and COD retention at 4 bar were 189.66 L/(m2·h) and 43.03%, respectively. NF membranes showed higher COD and conductivity retentions than UF membranes. The COD retention of Desal5-DK reached 98.3% at 20 bar. Lastly, the flux recovery after the filtration test of each membrane is also discussed.