Drought has become a commonly natural hazard in nearly all regions of China, while, it has caused serious destructive effects on agriculture, ecological environment and residents. Climate change is ever increasing the frequency and intensity of droughts. Alternatively, the increase in CO2 concentration can alleviate the occurrence of droughts, and reduce the drought frequency and severity. Therefore, it is crucial to investigate the occurrence of drought under different climate scenarios and the mitigation effect of increased CO2 concentration in the future. In this study, the meteorological data were downloaded from 5 GCMs’ simulations from the sixth phase of the coupled model intercomparison project (CMIP6), and then to downscale using the bias correction and spatial disaggregation (BCSD), finally to integrate the downscaled climatic data using Bayesian modelling averaging (BMA). A drought trend was analyzed considering and without considering the effect of CO2 under the SSP2-4.5 and SSP5-8.5 scenarios using the standard precipitation evapotranspiration index (SPEI). The results show that the BMA average model improved the simulation accuracy, and stability of precipitation and temperature. The correlation coefficient with the measured precipitation was greater than 0.8, and that with temperature was greater than 0.98. Both SSP2-4.5 and SSP5-8.5 scenarios showed a strong warming trend across China. By the end of the 21st century, the temperature increased by 2.7 and 6.2°C under the SSP2-4.5 and SSP5-8.5 scenarios. The precipitation also showed a significant increase across China. The annual precipitation in the SSP5-8.5 and SSP2-4.5 increased 150 and 50 mm, respectively. The increase of temperature resulted in a continuous increase in the potential evapotranspiration (PET), but the increasing trend of PET considering the influence of CO2 concentration (PET[CO2]) slowed down significantly. The higher the CO2 concentration, the more obvious the slowing trend. SPEI presented an obvious downward trend across China, where the downward trend in northwest China was the most significant, with a more severe trend under the SSP5-8.5 scenario than the SSP2-4.5 scenario. The drought area ratio in Northwest China also showed the strongest increasing trend, especially after 2070. By the end of the 21st century, the drought area ratio exceeded 80% under SSP5-8.5 scenario in the northwestern desert of China. The variation trends of the drought area in the Qinghai-Tibet Plateau, northeastern China, central China, and southern China are more consistent. Under the SSP5-8.5 scenario, the drought area ratio showed an increasing trend, but under the SSP2-4.5 scenario, the drought area ratio calculated by SPEI showed no obvious trend, while the drought area calculated by SPEI[CO2] showed a slight downward trend. Under the SSP5-8.5 scenario, the drought area ratio of the whole mainland China showed an overall increasing trend, and the drought area ratio calculated by SPEI[CO2] under the SSP2-4.5 scenario showed a slow downward trend. In conclusion, under the same scenario, the drought index that does not consider the impact of CO2 overestimates the future occurrence of drought. More efforts may be needed to mitigate the consequent impact there under climate change. The results of this study emphasize the importance that vegetation control land hydrological process through the response to future CO2 concentration increase, and indicate that the influence of CO2 on drought trend should be considered in future drought investigation, thereby to offer systematic and scientific fundamentals for the management of water resource. The findings can provide a scientific basis for adaptation strategies to promote drought preparedness and the implementation of reliable warning systems, thereby to quickly mitigate potential impacts of future droughts all over China.