To reveal the logical relationship between farmers' individual behavior and the generation and control policies of agricultural non-point source nutrient in watershed, scenario analysis approaches in watershed nutrient control policies are established based on coupling System Dynamic model with Multi-agent Agricultural household model for Rural Environmental Management model. This research took Pearl River Basin as the research object. This study designs four future scenarios:business-as-usual scenario, low fertilizer fax rate scenario, middle fertilizer fax rate scenario and high fertilizer fax rate scenario, simultaneously with the same pesticide tax rate of 25% for latter three policy scenarios. Under various scenarios, the response of watershed nutrient to agricultural policies is quantitatively described and optimal policy for controlling watershed nutrient is assessed. The results indicate that in low fertilizer fax rate scenario, middle fertilizer fax rate scenario and high fertilizer fax rate scenario for 2030, the quantity of synthetic fertilizer applied will be 24.0%, 39.8% and 50.2% less than that of in business-as-usual scenario, respectively; the quantity of pesticide applied will be 27.6%, 32.8% and 37.4% less than that of in business-as-usual scenario, respectively; crop yield will be 10.0%, 16.3% and 21.2% less than that of in business-as-usual scenario, respectively; the number of livestock will be 5.9%, 7.5% and 14.0% higher than that of in business-as-usual scenario, respectively. In business-as-usual scenario, low fertilizer fax rate scenario, middle fertilizer fax rate scenario and high fertilizer fax rate scenario for 2030, the total nitrogen input to Pearl River Basin will be 9.45×10⁵, 8.51×10⁵, 7.85×10⁵ and 7.53×10⁵ t, respectively; the total phosphorus input to Pearl River Basin will be 1.40×10⁵, 1.28×10⁵, 1.20×10⁵ and 1.16×10⁵ t. The combination of fertilizer tax rate and pesticide tax rate can effectively reduce the discharge of nutrient. Even though middle fertilizer fax rate scenario and high fertilizer fax rate scenario have greater control effects, they have marginal effect, higher economic cost, less crop production and more animal manure pollution compared to low fertilizer fax rate scenario. Therefore, the policy option carried out in low fertilizer fax rate scenario is considered to be optimal for controlling Pearl River's nutrient pollution.