The water footprints of main crops in Huaihe River Basin were discussed in order to provide a theoretical basis for the improvement of regional agricultural water use structure and water shortage. Taking the main crops in the five provinces of the Huaihe River Basin as the research objects, the spatial and temporal changes of the blue, green and gray water footprints of wheat, rice, maize, soybean and oil plants from 2000 to 2017 were calculated and analyzed, and the influencing factors of crop water footprints were explored using path analysis. The results show that the soybean had the largest annual average water footprint,and crop water footprints were negatively correlated with the yield per unit. In terms of inter-annual variability, the total water footprint of wheat, rice, maize, and oil plants generally showed a decreasing trend, whereas that of soybean showed a trend of fluctuated increase. As to the spatial distribution, the total water footprints in Anhui Province and Henan Province were the largest, the spatial distribution of the water footprint showed a certain degree of aggregation, which was generally high in the middle and low in the surrounding areas. In addition, the factors that had the greatest impact on the water footprint of crops in the Huai River Basin were the application amount of nitrogen fertilizers, average temperature and annual rainfall.