Abstract: Alluvial fan area is the main area of agricultural development, and also the sensitive area of nitrogen leaching. At present, the understanding of the spatial and temporal distribution of soil water and nitrogen leaching fluxes in deep soil at the scale of alluvial fan area is still limited. In this study, the farmland in the north of the alluvial fan of Hutuo River is selected as the main research area. Based on the improved HYDRUS regional scale water and nitrogen flux simulation model, the soil water and nitrate nitrogen transport processes in the regional farmland from 1975 to 2021 are simulated in parallel. The results show that: Different crop types were one of the main factors affecting soil nitrogen accumulation and flux in the study area. The average annual nitrogen accumulation of main crop types was in descending order: vegetable area (2 432 kg·hm⁻²∙a⁻¹)> wheat-maize rotation (1 508 kg·hm⁻²∙a⁻¹)> cotton (1 504 kg·hm⁻²∙a⁻¹)> orchards (364 kg·hm⁻²∙a⁻¹). The average annual water fluxes of main crop types were in descending order: vegetables (351 mm∙a⁻¹)> wheat-maize rotation (98 mm∙a⁻¹)> orchards (87 mm∙a⁻¹)> cotton (54 mm∙a⁻¹). The average annual nitrogen loss of the main crop types was in descending order: vegetables (374 kg·hm⁻²∙a⁻¹)> wheat-maize rotation (68 kg·hm⁻²∙a⁻¹)> orchards (23 kg·hm⁻²∙a⁻¹)> cotton (21 kg·hm⁻²∙a⁻¹). Crop type affected the spatial distribution of soil water and nitrogen flux and the lag time of response of nitrate loss to surface nitrogen input. High irrigation and high fertilization for vegetable production resulted in the shortest lag time of nitrogen leaching, followed by wheat and corn, and the longest lag time of nitrogen leaching in cotton and fruit trees. Soil nitrogen accumulation and leaching loss from vegetables and wheat-maize were positively correlated with water recharge fluxes, but there was no significant correlation between fruit trees and cotton. The inter-annual and seasonal response of soil nitrogen leaching to precipitation was obvious. The peak value of soil nitrogen leaching occurred in the rainy season, and the peak value of soil nitrogen leaching occurred along with heavy precipitation. The research can provide scientific support for regional non-point source pollution prevention and control and groundwater quality protection.