Abstract. Frequently happened meta-droughts have arisen broad social attention under current global climate change. A paleoclimatic perspective is expected to gain our understanding on the causes and manifestation more comprehensively. Southwestern China has been threatened by severe seasonal droughts. Our current knowledge of millennial-scale drying/wetting processes in this region is primarily based on the variability of the Indian Summer Monsoon. However, water availability over land does not always follow the monsoonal precipitation but also depends on water loss from evaporation and transpiration. Here, we reconstructed precipitation intensity, lake hydrological balance and soil water stress index (SWSI) covering the last 27,000 yr, based on grain size, geochemical and pollen records from Yilong Lake, to discuss the long-term nexus and discrepancies of dryness/wetness patterns in meteorological, hydrological and soil systems in central Yunnan region, SW China. Our results show that the long-term change trajectories among precipitation, hydrological balance and soil moisture were not completely consistent. During periods of low precipitation, hydrological balance and soil moisture were primarily controlled by temperature-induced evaporation change. This caused opposite status of precipitation with hydrological balance and soil moisture during the Last Glacial Maximum and Younger Dryas. During periods of high precipitation – the early to late Holocene, intensified evaporation from the lake surface offset the effects of increased precipitation on hydrological balance. But meanwhile, abundant rainfall and dense vegetation canopy avoided soil moisture deficit that might result from rising temperature. To sum up, hydrological balance in central Yunnan region was more vulnerable to temperature change while soil moisture could be further regulated by vegetation changes on millennial scale. As such, under future climate warming, surface water shortage in central Yunnan region can be even more serious. But for soil systems, efforts to reforestation may bring some relief to soil moisture deficit in this region.