This article is based on the recycling process of water resources, by studying on the circulation system of water resources, we determined 10 factors that lead to the shortage of water resources from three aspects: supply, usage and recycling, then the risk assessment system of water resources shortage is carried out. By using principal component analysis we analyzed the hydrological data from 1979 to 2014 in Beijing, determine the importance of each factor in the system, then established the calculation formula of risk coefficient. Finally, we divided into five equal probability risk interval as risk levels by studying the probability distribution of risk coefficient.