Analyzing the characteristics of spatio-temporal variability of droughts and floods is very important to reducing losses and costs. Based on the monthly rainfall data from 1954 to 2014 collected from 32 meteorological sites in Yunnan province, the spatio-temporal variability and periodicity of drought and flood were analyzed using SPI,EOF, RBF spatial interpolation, and wavelet analysis. The results show that there is a tendency of drying in Yunnan province during the past 61 years (the slope of SPI is -0.0091/year), and the SPI clearly indicates a great fluctuation and a high frequency after 2000. General flood years, normal years and general drought years account for 88.52% of the total in the 61 years, and great drought years, extreme drought years and great flood years account for 4.92%, 3.28%, and 3.28%, respectively. Since 2003, furthermore, drought eventshave beenmuch more frequent and serious. Jinghong-Simao-Yuanjiangand the area northeast of the Zhanyisiteare the two regions where droughts occur more frequently than the other regions in Yunnan province. And three regions,namely, the west of Lincang-Dali-Huaping line, the area north ofthe Zhaotong site, and the southeast of Yunnan province are where floods appear frequently. The frequency of drought and flood events have good correspondence, but the frequency of drought events is slightly higher than that of flood events. The first mode of EOF analysis reveals that Yunnan province shows flood or droughtconsistency, possibly affected by large-scale climate characteristics. The second mode may be controlled by topographical factors, and the third mode may be caused by multiple factors, such as monsoon and general atmospheric circulation. The time coefficients of the first three modes also confirm the trend of drought in Yunnan province. The periodic oscillation of SPI series is concentrated in quasi-2, 6-,8-,18- and 28-years, with the period of quasi-28 years being the dominating period.