Land-use changes driven by socio-economic factors have significantly altered the nitrogen (N) flows and loads to the agricultural environment with rising pollution threats. The present study evaluated and compared the N budget using substance flow analysis (SFA) between the traditional crop system (wheat-maize rotation) and the currently dominant kiwifruit orchard system in a typical catchment in Northwestern China. Total N input, N uptake, soil N accumulation increment (0–100 cm), and losses to the environment in the kiwifruit orchard system were 1220, 162, 783, and 275 kg N ha⁻¹ yr⁻¹, respectively, which were 175%, −31.6%, 517%, and 248% higher than the traditional crop system. In the traditional crop system, the input and output of N were relatively balanced, and N-use efficiency (NUE) was high (53.5%), with a low pollution discharge rate (PDR; 25.0%). However, in the intensive kiwifruit orchard system, NUE was comparably low (13.3%), resulting in a huge N surplus (1058 kg N ha⁻¹) and high PDR (77.2%). The land-use change from the traditional cropland to the profitable and intensive kiwifruits orchard severely increased the N input (2.8 times) and greatly enhanced the N loading (2.5 times) to the environment. The nitrate content of the shallow groundwater samples collected from the kiwifruit orchard area exceeded the national standard for the drinking water (≤10 mg/L). Therefore, farmers should adopt an improved N management measure that pays close attention to soil N budget and reduce N application in the kiwifruit orchards, efficiently utilizing the nutrients and causing minimum damage to the environment.