In order to deeply treat pharmaceutical wastewater to meet the industrial water quality standard, the membrane flux change of the comprehensive pharmaceutical wastewater treated with advanced nanofiltration and reverse osmosis was studied. The operating condition, flux and water yield rate were studied in continuous and cyclic modes. According to the change of membrane flux, the treatment and cleaning scheme suitable for industrial application of membrane separation were determined. The results show that the daily physical wash time of nanofiltration membrane is 7 minutes, the wash time of intensive acid and alkali is 90 minutes respectively, the average flux is 16.1 L/(m2·h) in continuous mode and 7.7 L/(m2·h) in cyclic mode, and the water recovery rate is 73%. The daily physical wash time of reverse osmosis membrane is 12 minutes, the wash time of intensive acid and alkali is 90 minutes respectively, the average flux is 12.8 L/(m2·h) in continuous mode and 7.2 L/(m2·h) in cycle mode, and the water recovery rate is 74%. The research on advanced membrane treatment of pharmaceutical wastewater provides a theoretical basis for the industrial application.