As one of the pharmaceutical industries related to people’s livelihood and health，biopharmaceutical industry is a characteristic emerging industry with the trend of cluster development in the Yangtze River Delta. Now it has become the second largest pharmaceutical industry in the region in terms of quantity and output value，second only to chemical synthesis pharmaceutical industry. However，the five major bio-pharmaceutical industries based on the whole industrial chain will produce and discharge wastewater with different degrees of pollution in the production process of enterprises，which has become a key industry in the green transformation of the Yangtze River Delta. Moreover，the wastewater discharge efficiency of pharmaceutical manufacturing industry in the Yangtze River Delta varies greatly from region to region，which cannot meet the needs of ecological and environmental green integrated development in the Yangtze River Delta，and to a certain extent，it causes safety risks and hidden dangers to the regional water environment. At the same time，by comparing the similarities and differences of the biological pharmaceutical water pollution discharge standards in the Yangtze River Delta，it is found that the classification and discharge conditions of water pollutants in the local standards of biological pharmaceutical industry in the Yangtze River Delta are different. Shanghai took the lead in issuing the local standards for the discharge of water pollutants by biomedical research and development institutions，but the newly issued limit standards for the discharge concentration of water pollutants in Jiangsu biopharmaceutical industry are higher than those in Shanghai，Zhejiang and Anhui. The local differences of water pollutant discharge standards in the biopharmacology industry in the Yangtze River Delta are mainly caused by the low competition in the pharmaceutical manufacturing industry in the Yangtze River Delta，the inconsistent standards of environmental supervision and law enforcement，and the difficulty in eliminating the risks and hidden dangers of transboundary water pollution. Therefore，from the perspective of water security，the paper puts forward policy suggestions on the integration of water pollutant discharge standards in the Yangtze River Delta from the perspectives of economic means of administration and market，legal guarantee mechanism and information sharing mechanism，including increasing financial investment in local water pollution treatment and promoting third-party treatment of pharmaceutical industry pollution. Unifying the discharge standards of water pollutants and environmental law enforcement standards in the Yangtze River Delta with the “negotiation mechanism”；Establish a sharing platform for water pollutant discharge data and governance performance of Yangtze River Delta polluters.