Based on the statistical data of precipitation, runoff coefficient, per-capita water resources, GDP per capita, and population density from 2003 to 2013 in the 5 provinces of Huaihe River Basin, we conducted a comprehensive risk assessment of the water resources shortage in Huaihe River Basin and each province by building a risk assessment system and using the variable fuzzy model and entropy weight method. The results showed that the overall risk of water shortage in the Huaihe River Basin during 2003-2013 was relatively high and showed a trend of slow growth. The risk reached the highest in 2004 when the precipitation was little. During the ten years, the increase of risk in Henan province was the most pronounced, whereas Shandong province was relatively stable with the smallest increase of risk. Henan province had the highest degree of risk among the five regions in the Huaihe River Basin, reaching 3.52. It was followed by Jiangsu province and Shandong province, while Anhui and Hubei provinces had relatively low risks, which were 2.86 and 2.51 respectively. The analysis of the secondary indicators of water shortage risk revealed that Henan province faced the highest threat while Anhui province faced the lowest. Shandong province was the most vulnerable to water shortage while Hubei province was the least vulnerable. Jiangsu province was the most exposed to water shortage while Shandong province was the least exposed. Hubei province had the best restorability from water shortage while Henan province had the worst restorability. Moreover, population density, GDP per capita, and precipitation had a great impact on water shortage risk.