Lake Xinyun is a typical plateau lake with severe environmental problems due to agricultural activities. Its water environment and ecological conditions are crucial for sustainable development of surrounding regions. Therefore, quantifying the spatio-temporal variations of anthropogenic nitrogen and phosphorus inputs, and their influencing factors are important for lake restoration and basin management. Based on socio-economic statistical data, the human activity-based Net Anthropogenic Nitrogen and Phosphorus Inputs (NANI and NAPI) models were used to quantify the NANI and NAPI intensities in the Lake Xingyun Basin. The results showed that the mean values of NANI and NAPI in the study area during 1989-2020 were (14614±2196) and (3135±452) kg/(km²·a), respectively. They exhibited an upward trend followed by a downward trend over time, with peak values of 18076 and 3889 kg/(km²·a) occurring in 2015. In terms of spatial distribution, NANI and NAPI were relatively high except some low values in the eastern region. Fertilizer and food/feed inputs were identified as the largest sources of NANI and NAPI, accounting for 58.2%-63.8% and 30.5%-59.5%, respectively. Furthermore, based on model selection and variable importance analysis, economic crop yield and livestock density were found to be the most significant factors affecting the changes of NANI and NAPI. Therefore, to control nitrogen and phosphorus loss in Lake Xingyun Basin, it is needed to implement several source-control strategies such as adjusting planting structures and patterns, and accelerating transformation of economic models. The results of this study can provide a scientific basis for establishing effective comprehensive nitrogen and phosphorus management measures in Lake Xingyun Basin.