Comprehensive pharmaceutical wastewater was treated with advanced nanofiltration and reverse osmosis. The membrane flux change and cleaning effect were studied in single-stage and cyclic modes as the appropriate cleaning time, flux and water yield rate were measured. The results show that the daily physical wash time was 7 minutes to nanofiltration, the intensive acid and alkali wash time was 90 minutes respectively, the average flux was 16.1 L/(m_² h) in single-stage and 7.7 L/(m_² h) in circulation, the water yield rate was 73 %. The daily physical wash time was 12 minutes to reverse osmosis, the intensive acid and alkali wash time was 90 minutes respectively, the average flux were 12.8 L/(m_² h) in single-stage and 7.2 L/(m_² h) in circulation, the water yield rate was 74 %. The suiTab.treatment and wash schemes were suggested for industrial application of membrane separation to pharmaceutical wastewater according to the flux change.