Improper use of chemical fertilizers is an essential reason for diffused pollution of agriculture. Therefore, finding out influence factors of farmers in application of chemical fertilizers will play a significant role in controlling the diffused pollution of agriculture. Through field survey, a total of 340 samples in 4 counties of Chongqing Municipality were obtained. On the basis of these samples, an empirical study was carried out. The study results indicate that farmers’ application of chemical fertilizers is negatively correlated with farmers’ age, education level, male labor proportion, and soil fertility, while the annual family income, agricultural production population proportion, commodity trading characteristics, and scientific fertilizer application ability fail to pass the significance test. These results will provide reference for proper application of chemical fertilizers and controlling diffused pollution.