Drought is an extreme climate event with long duration of slow development, and the impact of climate change on drought is particularly significant, drought has become a global problem in a changing climate. Assessing the impact of climate change on the drought characteristics of Yunnan Province is particularly important. The drought conditions in Yunnan Province were analyzed by using the multi-time scale standardized precipitation index (SPI) and standardized precipitation evapotranspiration index (SPEI). The seasonal variation of two indexes and the characteristics of drought in the region were analyzed by using non-exceedance probability and runs theory, respectively. The results showed that the non-exceedance probability of SPEI (1) below and equal to -1.0 in the winter of 1961—1995 was 5.2%, and it was increased to 18.4% from 2066 to 2100;the non-exceedance probability of SPEI (6) below and equal to -1.0 was increased from 4.4% to 21.4%, SPEI (24) was increased from 7.0% to 25.7%. It was showed that due to climate change, serious droughts may occur in the future, and the medium and long-term droughts were more serious than shortterm droughts. Severe droughts caused by climate change during the winter and summer periods from 1961 to 1995 and from 2066 to 2100, and the severity of medium and long-term droughts was particularly strong during winter and summer. SPI and SPEI time series were applied to the runs theory and it was found that the drought intensity determined by SPEI (1) from 1961 to 1995 was 28.3, which reached 60.9 by 2066 to 2100, indicating that the climate changes had exacerbated the future drought. The results were instructive and practical for drought prediction and assessment in Yunnan Province, as well as its risk management and application decisions. At the same time, it can provide a scientific reference for the future dry farming ecological management and drought evolution prediction.