In this paper, the monthly precipitation data are from 1960 to 2014, the monthly natural runoff data are from 1956 to 2000, and the affected area data of flood and drought disasters are from 1960 to 2000 in the Huai River Basin. With the help of SPI and SSI drought index, M-K trend analysis and correlation analysis are used to explore the temporal characteristics of regional meteorological and hydrological drought, to reveal the response of hydrological drought to meteorological drought, and to analyze the relationship between drought indices and historical drought. The results show that the drought reflected by the SPI index is more severe than that by the SSI; the drought is the most frequent and the drought levels are very complicated in the 1960s; the drought frequency is low in summer and is high in autumn and winter. Besides, MK trend test shows that the trend of drought is not significant in the Huai River Basin. With the increase in the time scale, the correlation between SPI and SSI is increasing; the response time of the SSI to the SPI is 1~4 months in the adjacent stations; the response tends to be faster and more pronounced especially during the months of seasonal alternation. The drought-affected area is significantly expanding in the study area; SPI and SSI are negatively correlated with the drought-affected area, positively correlated with the flood-affected area, and the correlation with the flood-affected area is stronger.