Based on the data of 82 meteorological stations and six representative hydrological stations in four provinces in Southwest China (Guizhou, Sichuan, Yunnan, Chongqing), this paper uses standardized precipitation evapotranspiration index (SPEI) and standardized runoff index (SRI) to analyze the spatial and temporal evolution characteristics of drought in the study area from 1968 to 2018. Combined with the Southwest monsoon index and historical drought data, the correlation of drought and the applicability of different drought indices were verified. The results show that: (1) SPEI-12 in Southwest China shows a downward trend from 1968 to 2018, with a linear trend rate of −0.074/10a, and SPEI-3 has a downward trend in four seasons, the maximum linear trend rate being −0.106/10a in autumn;(2) The change in SRI-12 and SRI-24 value directly reflected the decrease in SRI value, indicating that drought events are increasing in recent times, especially in the 21st century (3). Severe drought occurred in the south of Southwest China, as indicated by the increase of drought frequency in this area. The main reason for the variations in the frequency distribution of drought in Southwest China is the combined effect of the change of precipitation and evapotranspiration. (4) The correlation between hydrological drought index and disaster areas is stronger than the correlation between meteorological drought and disaster areas. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.