The non-point source pollution caused by nitrogen loss from fertilization has become the main factor in water pollution. Identifying and evaluating the environmental risks of nitrogen application is an important prerequisite for water pollutant prevention. This study focuses on the watershed above Hongze Lake of the Huaihe River, an improved minimum cumulative resistance model based on the "source - sink" theory in landscape ecology. On the one hand, the source risk of nitrogen non-point source pollution is evaluated by fertilization environmental risk index based on the amount of nitrogen applied. On the other hand, elevation, slope, land use, terrain moisture index, rainfall erosivity, and soil erodibility are selected as key resistance factors affecting the migration of non-point source pollution to construct a comprehensive resistance base, and an innovative approach is proposed to construct the sink risk of nitrogen non-point source pollution based on flow concentration routing. Finally, the comprehensive risk index of nitrogen non-point source pollution was formed by combining source risk and sink risk, and the risk level of non-point source pollution in the study area is classified. The results show the following. ① The source risk value of nitrogen non-point source pollution in the study area is 0~0.70, with an average value of 0.53. There is a widespread situation of excessive fertilization in the research area, especially in Shangqiu City, Zhoukou City, Zhumadian City, and Xinyang City within Henan Province. ② With the effect of various resistance factors, the resistance base shows a spatial trend of gradually decreasing from southwest to northeast. The sink risk shows a decreasing trend around the main stream. Moreover, the sink risk in the north part of the main stream is significantly lower than that in the southern region, since it has a longer flow routing. ③ The comprehensive risk index indicates that 71.04% of the entire study area is above the middle risk level, and the study area are facing serious nitrogen non-point source pollution issue. ④ Extremely high risk areas are mainly concentrated in the upper reaches of the main stream, such as Xinyang City and the northern part of Zhumadian City. There are large areas of high risk areas in Zhoukou, Shangqiu, Fuyang, Suzhou, and Bozhou cities, which located in the north part of the main stream. Low risk areas are mainly distributed in the mountainous areas of the headwaters of the main and tributary rivers. This study proposes specific prevention and control measures based on comprehensive risk of nitrogen non-point source pollution at different levels, which can provide decision-making basis for scientific prevention and effective management of agricultural non-point source pollution at the watershed scale.