Abstract: Non-point source pollution can often be caused by nitrogen loss from fertilization in the water system. It is very necessary to identify and evaluate the environmental risks of nitrogen application for water pollutant prevention. In this study, an improved model was proposed to minimize the cumulative resistance, according to the "source-sink" theory in landscape ecology. The watershed was also selected above Hongze Lake of the Huaihe River. The source risk of nitrogen non-point source pollution was evaluated by the fertilization environmental risk index when the amount of nitrogen was applied. The key resistance factors were selected as the elevation, slope, land use, terrain moisture index, rainfall erosivity, and soil erodibility. The migration of non-point source pollution was used to construct a comprehensive resistance base. An innovative approach was proposed to construct the sink risk of nitrogen non-point source pollution using flow concentration routing. Finally, the comprehensive risk index of nitrogen non-point source pollution was formed to combine the source and sink risk. The risk level of non-point source pollution was also classified in the study area. The results show the following. 1） The source risk value of nitrogen non-point source pollution was 0-0.81, with an average value of 0.55. There was a widespread situation of excessive fertilization, especially in Shangqiu, Zhoukou, Zhumadian, and Xinyang City within Henan Province. 2) The resistance base shared a spatial trend of gradually decreasing from the southwest to the northeast under various resistance factors. A decreasing trend of sink risk was observed around the main stream. Moreover, the sink risk in the north part of the main stream was significantly lower than that in the southern region, due to the longer flow routing. 3) The comprehensive risk index demonstrated that 71.16% of the entire study area was above the middle-risk level. There was serious nitrogen non-point source pollution in the study area. 4) Extremely high-risk areas were mainly concentrated in the upper reaches of the main stream, such as Xinyang City and the northern part of Zhumadian City. There were large areas of high-risk areas in Zhoukou, Shangqiu, Fuyang, Suzhou, and Bozhou cities, which were located in the north part of the main stream. Low-risk areas were distributed mainly in the mountainous areas of the headwaters of the main and tributary rivers. Specific prevention and control measures were proposed, according to the comprehensive risk of nitrogen non-point source pollution at different levels. The finding can also provide the decision-making basis for the scientific prevention and effective management of agricultural non-point source pollution at the watershed scale.