By using improved fuzzy synthetic evaluation and grey relational analysis models, water shortage risk of Beijing City that is one of water intake areas of South to North Water Diversion Project were evaluated. To determine evaluation index weights, the combined weight method was adopted. The results indicated that the risk of water shortage in Beijing was generally on the downward trend and tended to be stable during the year 2001—2014, and the shortage of water resources was reduced from higher risk to critical risk and lower risk, which indicated in recent years, the management and regulation of water resources by the Beijing municipal government have shown remarkable results. However, water shortage risk showed an upward trend after the year 2012, therefore close attention should be paid to the risk of water shortage in the coming years and measures should be taken as soon as possible so as to reduce the risk of water shortage in Beijing city and ensure water supply security in Beijing area.