Abstract: With the continuous strengthening of industrial and domestic pollution control in urban areas of the Yangtze River Basin in China, the contribution rate of non-point source (NPS) pollution has significantly increased. Utilizing relevant technology combinations to effectively control urban NPS load and improve water ecological environment quality has been the main content in urban areas of the Yangtze River Basin. In order to explore the effectiveness of NPS pollution control technology and facilities in reducing pollution and urban runoff in hilly areas of the Yangtze River Basin, this article took certain part of the New City Area of Yongchuan District, Chongqing as the research object to generate a catchment area. The Storm Water Management Model (SWMM) was constructed, and the parameters were determined and verified. The model was used to simulate four types of single Low Impact Development (LID) facilities, including permeable pavement, green roofs, rainwater gardens, and sunken green space, and nine combination schemes to reduce rainfall runoff and pollutant loads (including SS, COD, TN, NH₃-N, and TP) in the study area. From the perspectives of benefits, economy, and technology, the Analytic Hierarchy Process (AHP) based on cluster analysis was adopted to evaluate the effectiveness of various combination control schemes on the rainfall-runoff water process. The results showed that: the error of the hydrological and hydraulic parameter calibration results of the SWMM model in the research area was less than 1%, the Nash-Sutcliffe efficiency coefficients of the water quality parameters calibration results were all above 0.7, and B% MSSE index was close to 0, achieving the localization of model parameters. Under different designed rainfall scenarios, permeable pavement had the best control effect on runoff volume and runoff pollution load among the four single facility schemes. Based on a comprehensive evaluation from the perspectives of benefits, economy, and technology, plan P7 had been determined as the optimal combination plan for reducing NPS pollution in the study area. P7 had a layout area ratio of 35% permeable pavement, 30% green roof, 7% rain garden, and 30% sunken green space. The total runoff reduction rate reached 29.4%, and the reduction rates of SS, COD, TN, NH₃-N, and TP loads reached 36.2%, 35.1%, 35.1%, 30.6%, and 32.2%, respectively.