Chongqing agriculture and rural environment management and protection is not only an important part of constructing ecological civilization, achieving green development, sharing development achievements, but also the support to ecological defense of the Upper Reaches of Yangtze River. The situation of agriculture, rural environment governance and protection in the future of Chongqing is relatively serious. According to the feature of basic situation of Chongqing, rural development trend brings new pressure and threat to environment management and protection but faces new opportunity and challenge. During the 13 five-year plan period, the overall idea of Chongqing’s agriculture, rural environment management and protection should be sharing-based, ecological accumulation, urban-rural integration, national penetration, innovation-driven, multiple integration, and the construction of ecological civilization institution system with clear equity, multiple participation, equal-emphasis on incentive-constraint and complete system.