Quantifying the relative influences of anthropogenic activities and climate change on soil erosion and deposition during the Holocene, when both forces have been interacting is a complex problem. Analysis of long-term patterns in soil erosion and lake deposition in a basin can provide the basis for untangling the complexities of climate and anthropogenic forcings. In this paper, sedimentary sequences from Xingyun Lake are compared with simulated soil erosion rates in the basin to explore the relationship between river basin soil erosion and lake deposition during the Holocene in Yunnan, China. Modern soil erosion rates are calculated using RUSLE, while Holocene soil erosion rates are estimated using modern rates with reconstructed precipitation and vegetation cover sequences. Through this investigation, we found the following results. First, Holocene vegetation in the lake basin was mainly affected by climate change, and the vegetation experienced the same pattern of changes as the climate. Soil erosion and lake deposition rates, along with changes to vegetation cover, were synchronous with precipitation trends during the Holocene. Second, soil erosion and lake deposition have been exacerbated by human activities, such as deforestation and land reclamation in the Xingyun Lake basin. Finally, this study provides new insights into the effects by anthropogenic impacts and climate forcing on the processes of soil erosion and lake deposition on the millennium scale.