The daily temperature, precipitation of 149 meteorological stations and historical drought disaster in the Huai river basin from 1962 to 2016 were analyzed based on Standardized Precipitation Evapotranspiration Index (SPEI), Empirical Orthogonal Function and Mann-Kendall method. In this study drought evolution were analyzed and revealed the impact of agricultural production in the Huai river basin. The results showed that:(1) The correlation between the number of droughts and drought-affected area at the 0.05 significance level, indicating that the SPEI has an excellent suitability in the Huai river basin. (2) The drought time was significantly different and drought frequency was obvious fluctuation in the Huai river basin. The most of severe drought and extreme drought is the largest in 1960s (24.8%), followed by 2010s (15.8%) and lowest in 1980s (10.0%). (3) The spatial distribution of drought has much difference. The drought severity was change between 27.76% and 36.04% in the Huai river basin. The drought severity in the northwest and southeast is lower than that in the southwest, northeast and central regions. (4) The results showed that trend of regional drought had a tendency towards drought conditions, which was the decreasing from the middle to the surroundings in the Huai river basin. The principal modes of our results indicated obvious variation and consistent.