The characteristics of drought at different time scales between 1997 and 2012 in Yunnan Province were studied using a new drought index (standardized precipitation evapotranspiration index, SPEI) calculated based on daily precipitation data from 74 weather stations. In addition, we used a time series data set (1999-2013) of the normalized difference vegetation index (NDVI) and time series analysis to assess temporal dynamics of the NDVI, and we explored the relationships between NDVI and SPEI. Correlations between NDVI and multiscale SPEI were examined, including annual, monthly, and seasonal long-term dynamics. Annual average and annual maximum NDVI in Yunnan Province showed an upward trending wave shape with slopes of 0.0017 and 0.0011, respectively. Monthly NDVI showed the same pattern, and the wave crest in each year was concentrated in July through September. Interannual variability in the NDVI showed significant seasonal differences, with higher NDVI in summer and autumn compared to spring and winter. A relatively consistent and dynamic trend was found in the time scales of mean annual SPEI. Drought intensity increased in small increments from 1997 to 2012, and the trend was more obvious at larger time scales. The 3-month SPEI value (SPEI3) initially increased and then decreased, and its wave crest was concentrated in May through July. The seasonal SPEI3 value reflected the level of drought strength as follows: winter > autumn > spring > summer. We found that the correlation between NDVI and SPEI at different time scales was complex and variable. The relationship between annual average NDVI and annual SPEI was weak, while the annual maximum NDVI and annual SPEI were positively correlated, especially for SPEI3, SPEI6, and SPEI12. No significant correlation was observed between monthly NDVI and SPEI; in contrast, years with average monthly NDVI showed a strong response to SPEI at different time scales. The coefficients between years for average monthly NDVI and SPEI were strongly affected by the SPEI time scale, with a 1- and 2-month lag. The NDVI in autumn and winter showed a strong negative correlation with SPEI for the same season, and the autumn NDVI was slightly correlated with SPEI in summer of the same year. The lag effect was also found in other seasons to different extents.