[Objective] The “source-sink” risk pattern of non-point source (NPS) pollution in the upper reaches of the Erhai Lake basin was identified in order to provide a theoretical basis for protecting the ecology of Erhai Lake and for rapidly identificatiing key areas of “source-sink” NPS pollution risk. [Methods] An evaluation system of resistance base surfaces was built based on data from 2005, 2010, 2015, and 2020. Resistance surfaces were established and NPS pollution risk levels were classified based on the minimum cumulative resistance model to analyze changes in NPS pollution risk levels over these 16 years in the upper reaches of the Erhai Lake basin. [Results] ① Spatial heterogeneity in the resistance factor caused regional differences in the distribution of the resistance base surfaces, while the distribution of the “source” affected the distribution of the resistance surfaces. The resistance surfaces value increased by 7 485.40 from 2005 to 2020. ② Thirty percent of the study area was classified as extremely high-risk zones, while the area of the medium-risk zones accounted for more than 60% of the study area, and the NPS pollution risk level was high. During the 16 years of the study, the area of extremely high-risk zones decreased the most (35.74 km²), while the area of medium-risk zones increased the most (38.69 km²). ③ The closer the NPS pollution risk level was to the “source”, the higher the risk level. The risk level was higher in the central region than at the border, and higher in the south than in the north, while the extremely high-risk zones were the key area of NPS pollution. ④ Among zones of different risk levels, the medium-risk zones witnessed the largest transfer-out (80.93 km²) in the past 16 years. The main transfer-out areas were the intersections of three towns (Cibi Lake, Fengyu, and Yousuo) and the northern part of Niujie Town. [Conclusion] Measures such as landscape optimization and planting adjustments in key zones have a more positive effect on reducing the loss of nitrogen and phosphorus and changing the risk level pattern, which could further improve the future water environment of the Erhai Lake.