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The rapid increase in the proportion of cash crops and livestock production in the Yangtze River Basin has led to commensurate increases in fertilizer and pesticide inputs. Excessive application of chemical fertilizer, organophosphorus pesticides and inappropriate disposal of agricultural waste induced water pollution and potentially threaten Agriculture Green Development (AGD). To ensure food security and the food supply capacity of the Yangtze River Basin, it is important to balance green and development, while ensuring the quality of water bodies. Multiple pollutants affect the transfer, adsorption, photolysis and degradation of each other throughout the soil-plant-water system. This paper considers the impact of multi-pollutants on the nitrogen and phosphorus cycles especially for crops, which are related to achieving food security and AGD. It presents prospective on theory, modeling and multi-pollutant control in the Yangtze River Basin for AGD that are of potential value for other developing regions. [ABSTRACT FROM AUTHOR]