Different crops can generate different non-point source (NPS) loads because of their spatial topography heterogeneity and variable fertilization application rates. The objective of this study was to assess nitrogen NPS load reduction efficiency by spatially adjusting crop plantings as an agricultural conservation management (ACM) measure in a typical small agricultural watershed in the black soil region in northeast China. The assessment was undertaken using the Soil and Water Assessment Tool (SWAT). Results showed that lowland crops produce higher nitrogen NPS loads than those in highlands. It was also found that corn gave a comparatively larger NPS load than soybeans due to its larger fertilization demand. The ACM assessed was the conversion of lowland corn crops into soybean crops and highland soybean crops into corn crops. The verified SWAT model was used to evaluate the impact of the ACM action on nitrogen loads. The results revealed that the ACM could reduce NO3-N and total nitrogen loads by 9.5 and 10.7%, respectively, without changing the area of crops. Spatially optimized regulation of crop planting according to fertilizer demand and geological landscapes can effectively decrease NPS nitrogen exports from agricultural watersheds.