In recent years, the research on non-point source (NPS) pollution has been deepening, but it is focused on the large-scale watershed or region. There are a few studies on the scales of small watershed and runoff plot, and it is even less to analyze the characteristics and mechanism of non-point source pollution in certain watershed by combining three different scales. Based on the combination of natural rainfall monitoring and MIKE model simulation, the Shaanxi section of Hanjiang River Basin in China was taken as an example to study the characteristics of NPS pollution at different spatial scales. The results showed that there was an obvious correlation between rainfall and runoff/sediment yield. The order of runoff yield/sediment yield per unit area was as follows: woodland > forested and grassy land > arable land. There was a significant relationship between the loss of total phosphorus and the sediment yield in the runoff plots. The total nitrogen pollution was serious, with an average concentration of 3.8mg/L. The nutrient loss was in the form of nitrate nitrogen, with an average proportion of 63.06%. For small watershed scale, the characteristics of rainfall runoff pollution generation were like runoff plot scale, both have obvious initial scour phenomenon. However, compared with runoff plot scale, the pollutant loss concentration increases with a strong lag. The MIKE model based on the coupling of hydrology, hydrodynamics, and pollution load had a strong applicability in the basin. The critical source areas of NPS pollution were identified, and five scenarios were laid out in the areas for the control of NPS pollution. Centralized livestock and poultry farming had the best reduction effect.