Non-point source pollution arises from fertilizer application in China. This paper empirical test the major factors which affect fertilizer application amount using econometric models and micro-level data from Jianghan plain in Hubei province by year 2006. The results demonstrate that housemaster’s education level, family’s management scale, land fragmentation are major factors affecting farmer’s decision-making process. When farmers have consciousness of scientific fertilization, higher agricultural labor proportion, farther land distance, longer production period could decrease fertilizer application amount. In the field of agricultural public policy, training for technical generalization is helpful in reducing fertilizer consumption.