Based on the meteorological observation data at seven national stations in Chuzhou of Anhui Province from 1961 to 2019 and the observation data in growth periods and yield per unit area of wheat from 1980 to 2019, the characteristics of meteorological drought and flood in Chuzhou and its impact on wheat yield were discussed and analyzed by using the multi-time-scale SPEI. The results show that the monthly and seasonal variation characteristics of SPEI were obvious in Chuzhou, and the astringency of SPEI in each month of winter was the strongest, while the dispersion of SPEI in each month of summer was the biggest. The climate characteristic of drought in spring and flood in summer was obvious in Chuzhou. The continuous drought from spring to summer was the most serious seasonal continuous drought in Chuzhou, and the continuous flood from spring to summer was the most serious seasonal continuous flood in the whole year. There was a trend of drought in spring since 2000 in Chuzhou, and the climate in summer and winter became wet after the 1990s, especially in winter, while the trend of dry and wet in autumn wasn’t significant, but there was a slight humidifying trend after 2009. The correlation between SPEI3 in March and wheat climate yield was the most significant, and there was parabola relationship with negative quadratic coefficient between them. When the value of SPEI3 in March was greater than 0.81 or less than -1.93, the yield of wheat was likely to reduce highly.