Taking Huaihe river basin as example, the precipitation, land utilization, economy and population were selected as rainstorm and flood risk indexes and their importance was determined by modified Analytic Hierarchy Process (AHP) based on comentropy. The application of improved AHP in the county-scale rainstorm and flood risk shows that (1)The spatial distribution of rainstorm and flood risk in Huaihe river basin appears high in the south but low in the north; high in the east and west and followed by the middle. (2) The area of high risk regions and the number of cities and counties in this region evaluated by the modified AHP all decreases compared with traditional methods, but the area of the secondary high risk regions, medium risk regions, secondary low risk and low risk regions all increase. Meanwhile, the rising of the average risk possibility may lead to the increasing of disaster degree. (3)The risk grade deduced by the improved method in Yuexi county is lower than that in Jinzhai county. In Suzhou, the risk grade descends from secondary high risk to medium risk, which is lower than that in Lingbi and Sixian and is more consistent with actual situation. Therefore, it is concluded that the modified AHP improves the precision of rainstorm and flood risk assessment in Huaihe river basion.