Agricultural non-point source pollution is an important problem for water environmental protection in China, and risk assessment is of great significance for the prevention and control of agricultural non-point source pollution. Taking Henan Province as the research area, a multi factor comprehensive evaluation model for nitrogen agricultural non-point source pollution was constructed, the hierarchical assignment method of Analytic Hierarchy Process was used, the weights of each influencing factor were determined based on entropy method and expert scoring, the risk index of nitrogen agricultural non-point source pollution in Henan Province was calculated, and it was verified at the basin scale. The risk level of nitrogen agricultural non-point source pollution was divided and critical control areas were identified. The results showed that planting, breeding and domestic sources contributed 31.52%, 38.47% and 30.01% of the nitrogen loss load, respectively. The nitrogen loss load was low in the west and high in the middle and east of Henan Province. In Henan Province, 39.429km2 area was at moderate risk, accounting for 23.61% of the total area of Henan Province, and 17.318km2 area was at high risk, accounting for 10.37% of the total area of Henan Province. The medium and high-risk zones within 2km from the river were classified as general control areas and key control areas, with the general control area of 10.982km2 and the key control area of 9.285km2. Correlation analysis was carried out between the model and the data of automatic water quality monitoring stations in Henan Province in 2021 at the basin scale, and the fitting degree R2=0.82, indicating that the model had a high accuracy. The results showed that the multi-factor comprehensive evaluation model established was scientific and accurate, which can be used for the identification of nitrogen agricultural non-point source pollution.