Based on CN05.1 observation grid data and Coupled Model Intercomparison Project Phase 6 (CMIP6) model simulation data, the study comprehensively evaluated the simulation capability of CMIP6 models for self-calibrating Palmer Drought Severity Index (scPDSI) in China, and selected 7 models ensemble with relatively good performance to project the change characteristics of scPDSI, runoff and soil moisture in China in the 21st century, and on this basis, the study analyzed the uncertainty of CMIP6 future projection. The results show that the simulation capability of CMIP6 models for scPDSI over China still needs to be improved, the simulation performance of MME is better than most individual models, but there are still deficiencies in temporal trend and amplitude. The temporal trend of scPDSI shows a slight increasing trend under SSP1-2.6 and SSP2-4.5 scenario, the trend values are respectively 0.03/10a and 0.01/10a, and a decreasing trend under SSP5-8.5 scenarios (-0.05/10a). Soil moisture show decreasing trends over time, the trend values of top-10-cm-layer soil moisture and total soil moisture are -0.30%/10a and -0.26%/10a in the SSP5-8.5 scenario, respectively. Runoff show increasing trends over time, the trend values of surface runoff and total runoff are 1.76%/10a and 3.13%/10a in the SSP5-8.5 scenario, respectively. At the end of the 21st century, the annual scPDSI over China generally decreases under higher emission scenarios, the change of soil moisture is generally "high in the North and low in the South", the downtrend is most significant in the Qinghai-Tibet Plateau region, and the change range of surface soil moisture is bigger. Runoff tends to rise in most areas, except Northwest China and the Qinghai-Tibet Plateau region, and the change range of it is bigger under higher emission scenarios. The probability density curves of most variables in the 21st century flatten under higher emission scenarios, so that the future changes become more dramatic.