Using the survey data on 340 farmers in Chongqing City, this paper performs an empirical analysis of the factors influencing the non-point source pollution of pesticides. The results show that the older householders will apply more pesticides, which may be due to the weak physical strength and weak ability to accept the concept of advanced cultivation; the householders with high level of education will choose to use less pesticides; the pesticide application rate is negatively correlated with whether farmers have participated in agricultural technology training, that is, the farmers having participated in agricultural technology training have stronger ability to scientifically apply pesticides, and in-depth understanding of advanced agricultural production technology and positive and negative effects of pesticides, so they often choose to reduce the application rate of pesticide; the cognitive factor on the role of pesticides in better promoting the growth of crops is significant, which requires the government and relevant departments to carry out concrete publicity of effectiveness and negative impact of different pesticides during the popularization of agricultural science knowledge, to prompt farmers to have a systematic and in-depth understanding of the agricultural non-point source pollution caused by pesticides.