Abstract: Danjiangkou reservoir area was the core water source area of the middle route of the South-to-North Water Transfer Project, It was the premise to strengthen the risk control of chemical fertilizer application to comprehensively understand the spatial difference of chemical fertilizer application and its potential threat to ecological environment. This paper used environmental risk assessment model to evaluate the environmental risk of chemical fertilizer application of main crops in different areas of Shiyan city in 2020. The results showed that the total amount of chemical fertilizer applied to main crops reached 8.97×104 t in 2020 and compound fertilizer was the largest type. The comprehensive fertilizer application amount of corn and potato accounted for 50.37% of the total input of the city, which were the largest fertilizer consumption crop type. wheat and rapeseed followed, while rice, peanuts and pulses accounted for a relatively small proportion. The environmental risk of chemical fertilizer application among demonstrated significant different patterns of spatial distribution in Shiyan. The two areas with the largest amount of fertilizer input were Yunyang and Zhushan, while the two smallest were Zhangwan and Maojian. The distribution characteristics of chemical fertilizer on crops were not consistent in different regions, which could be roughly divide into three types: wheat-corn rotation system dominant type, corn+potato intercropping system dominant type and corn-rape rotation system dominant type. The average intensity of fertilizer application per unit sown area in Shiyan city was 343.07 kg·hm-2, which had exceeded the standard of fertilizer application for China’ ecological county constructions(250 kg·hm-2) and was 1.52 times of the upper limit of environmental safety standard of fertilizer application in developed countries. The risk level of fertilizer application in most areas of Shiyan were “medium”, but it has entered serious state. in Zhushan and Zhangwan. The overall risk index of fertilizer application was 0.697, which was still at the medium risk level, but there were hidden dangers that might change into severe risk. And the environmental risk of nitrogen fertilizer and phosphate fertilizer application had entered a severe risk level, while it was at a lower level of medium risk of potassium fertilizer. Excessive intensity of chemical fertilizer application in the water source area was caused by a wide range of sources. The relevant government departments should take effective measures based on the load sources of fertilizer in different regions from the aspects of fertilization techniques, policy guidance, mechanism incentive and concept renewal, so as to achieve the dual goals of “reducing fertilizer application and improving efficiency” and “preventing and controlling environmental risks” simultaneously.