The spatial heterogeneity of human activity is fundamental for understanding regional human-land relations and its ecological environmental effects. Utilizing 2020 land-use data from nine plateau lake basins in Yunnan Province, we developed human impact intensity coefficients for varying landscape types. Employing GIS spatial analysis, this study quantified the intensity and spatial heterogeneity of human activities in the basins, and studied its effect on water quality. The study identified a descending order of human activity intensity(HAI) on the lakes as follows: Lake Qilu (4.83), Lake Xingyun (4.71), Lake Dianchi (4.19), Lake Yangzonghai (4.11), Lake Fuxian (4.03), Lake Yilong (4.01), Lake Chenghai (3.93), Lake Erhai (3.88) and Lake Lugu (2.96). The discernible spatial variation of human activity intensity was observed at three scales: watershed, flat area, and lakeshore. Each basin was influenced by strong human activity, and maximum values occurred in the flat area. A portion of the lakeshore of Lake Dianchi and Lake Qilu was fully developed area. HAI decreased with increasing elevation and slope, and high-intensity areas were concentrated around lakes with low elevation and flat land in the basin. The significant positive correlation between the high-intensity areas on the scale of the watershed and flat area on the trophic state index of the lakes, thus it should be the key area of landscape optimization and management in the future. Lakeshore scale low-intensity occupancy was significant negative correlation, and there is a need to reduce human activities. Considering the cascade effect of topography and geomorphology of the watershed - intensity of human activities-water quality, the control of each landscape element and process should be carried out from different spatial scales. According to the effects from various human activity intensity on the water quality, lakes can be classified into the preventive type, protective type and treatment type for their management.