Abstract: The middle and lower reaches of the Yangtze River is the main area for rice and wheat producing in China. To clarify the environmental effects of agricultural production in this area can provide theoretical guidance for the realization of green agricultural development. In this study, we analyzed and evaluated the resource consumption and pollutant emission inventory of rice winter wheat rotation system in Nanjing, Jiangsu based on a method of life cycle assessment. Results indicated that the major environmental effects of the life cycle in rice season were eutrophication, water toxicity, environmental acidification and soil toxicity, with the environmental impact indices of 2.32, 0.76, 0.33 and 0.27, respectively. While in wheat season, eutrophication, water toxicity, soil toxicity and environmental acidification were the major environmental impacts, with the environmental impact indices of 2.50, 2.09, 0.32 and 0.24, respectively. The production and use of fertilizers, pesticides and diesel oil were the main factors for energy consumption and climate warming. The key to the potential environmental acidification and aquatic eutrophication were the excessive nitrogen fertilizers application by farmers. The input of pesticides was the main cause of potential water ecotoxicity and soil ecotoxicity, and the input of nitrogen fertilizers and pesticides both have a greater impact on human toxicity. As a result, the negative environmental impact can be effectively controlled by development of new energy sources and implement cleaner production in the industrial field, and optimizing field management (such as reducing the application of nitrogen fertilizer, developing multifunctional integrated agricultural machinery and promoting low toxicity and high efficiency pesticides) in the middle and lower reaches of the Yangtze River.