With the rapid development of modern agriculture, agricultural non-point source pollution becomes increasingly serious in China, improving farmers’ environmental protection consciousness plays a very important role in the reduction of agricultural non-point source pollution. Therefore, this investigation and study chooses rural areas of five counties from Chongqing city and Zhejiang province as our samples, our investigation and statistical analysis includes the following four aspects: farmers’ cognition on non-point source pollution concept, farmers’ cognition to rural environment satisfaction, farmers’ cognition on non-point source pollution in agricultural production and farmers’ cognition on the consequences of agricultural non-point source pollution and the effects on ecological environment. The analysis and conclusions of farmers’ consciousness cognition on agricultural non-point source pollution, provides the supports in theory and practice for optimizing the behavior of farmers, promoting the management of agricultural non-point source pollution and implementing new rural construction goal.