Non-point source (NPS) pollution poses a significant threat to the water environment, yet controlling it at the watershed scale remains a formidable challenge. Understanding the characteristics and drivers of nitrogen (N) and phosphorus (P) outputs at the watershed scale, along with identifying cost-effective best management practices (BMPs), is crucial for effective pollution control. In this study, we utilized the Wangjiaqiao watershed within the Three Gorges Reservoir Area (TGRA) as a case study to explore the characteristics of N and P load outputs and their dominant drivers by combining the SWAT model and a geographic detector. Based on our analysis of N and P loads within the watershed, we employed the entropy weight method to evaluate the reduction efficiency and cost-effectiveness of 64 BMP scenarios, encompassing seven measures (vegetative filter strips, parallel terraces, 10% fertilizer reduction, 30% fertilizer reduction, residue cover tillage, grass mulching, and returning farmland to forest) and their combinations. Our findings revealed the following: (1) spatial heterogeneity in NPS loads within the watershed, primarily influenced by land use, fertilizer application, and surface runoff, with interactive enhancement effects among driving factors; (2) the differential effectiveness of BMPs at the watershed level, with structural measures, particularly terracing, exhibiting higher efficacy and achieving reduction rates of 28.12% for total nitrogen (TN) and 37.69% for total phosphorus (TP); the combined BMPs showed improved reduction efficiency, but not merely additive; and (3) in terms of cost-effectiveness, 30% fertilizer reduction emerged as the most beneficial among the individual measures. Moreover, a combination of vegetative filter strips, parallel terraces, and 30% fertilizer reduction demonstrated significant improvements in TN and TP reductions (48.05% and 61.95%, respectively), suggesting their widespread applicability. Overall, our study provides insights into developing a cost-effective BMP strategy for the Wangjiaqiao watershed and offers valuable guidance for NPS pollution management in similar small watersheds within the TGRA.