The large amount of fertilizers applied on the agricultural land around the Shuaishui Watershed is one of the main sources of the non-point source (NPS) load; therefore, it is of great significance to study different fertilization management for NPS-TN and NPS-TP control for the downstream Qiandao Lake water. The SWAT model was established to simulate NPS pollution under three fertilization scenarios: fertilizer reduction, manure substitution and deep fertilization. The results showed that the fertilizer reduction can reduce about 9.77% of the TN and 4.42% of the TP load. The NPS-TN load removal rate under deep fertilization is lower than that of the NPS-TP. Reduction rate of nitrogen and phosphorus load of manure substitution is low. The combined measure of fertilizer reduction and deep fertilization could reduce 10.11% for NPS-TN load and 8.38% for NPS-TP load, which is the best solution for fertilization management in the basin. In addition, the model-based fertilizer simulation management have guiding significance for reducing NPS pollution.