The Soil and Water Assessment Tool (SWAT) was utilized to analyze the spatiotemporal distribution patterns of composite non-point source pollution in the Yapu Port Basin, China, and to quantify the pollutant load contributions from various sources. Scenario-based simulations were designed to assess the effectiveness of different mitigation strategies, focusing on both agricultural and urban non-point source pollution control. The watershed was divided into 39 sub-watersheds and 106 hydrologic response units (HRUs). Model calibration and validation were conducted using the observed data on runoff, total phosphorus (TP), and total nitrogen (TN). The results demonstrate good model performance, with coefficients of determination (R²) ≥ 0.85 and Nash–Sutcliffe efficiencies (NSEs) ≥ 0.84, indicating its applicability to the study area. Temporally, pollutant loads exhibited a positive correlation with precipitation, with peak values observed during the annual flood season. Spatially, pollution intensity increased from upstream to downstream, with the western region of the watershed showing higher loss intensity. Pollution was predominantly concentrated in the downstream region. Based on the composite source analysis, a series of management measures were designed targeting both agricultural and urban non-point source pollution. Among individual measures, fertilizer reduction in agricultural fields and the establishment of vegetative buffer strips demonstrated the highest effectiveness. Combined management strategies significantly enhanced pollution control, with average TN and TP load reductions of 22.18% and 22.70%, respectively. The most effective scenario combined fertilizer reduction, improved urban stormwater utilization, vegetative buffer strips, and grassed swales in both farmland and orchards, resulting in TN and TP reductions of 67.2% and 56.2%, respectively.