The soil surface nitrogen balance (SSNB) method is commonly used to assess the nutrient use efficiency (NUE) of agricultural systems and any associated potential environmental impacts. However, the nitrogen flow of wide natural grasslands and other natural areas differ from that of artificial croplands and mown grasslands. In this study, we integrated root growth and the important nutrient resorption process into the SSNB model and used the improved model to clarify the nitrogen (N) flow and balance in the Three Rivers Headwater Region (TRHR)—an area dominated by alpine meadows—from 2012–2019. In the grassland system, the N surplus (ΔN) was 0.274 g m−2 year−1, and root return (BLD) dominated the N input, accounting for 67% of the total input (3.924 g m−2 year−1). N resorption was the main internal N flow in the grassland system (1.079 g m−2 year−1), and 30% of grassland uptake (NUP−grass). The ΔN of the agricultural system was 1.097 g m−2 year−1, which was four times that of the grassland, and chemical fertilizer was the largest input, accounting for 84% of the total input. The NUE in grassland was 93%, which suggests a risk of soil mining and degradation, while that of cropland was 76% and within an ideal range. The ΔN provides a robust measure of river N export, the TRHR was divided into three catchments, and the export coefficient was 16.14%–55.68%. The results of this study show that the improved SSNB model can be applied to a wide range of natural grasslands that have high root biomass and resorption characteristics.