In view of the problems existing in the development and utilization of water resources in Sanjiang Plain, this paper made a study on the risk assessment of water resources shortage in Sanjiang Plain. From the perspective of water resources shortage risk, analytic hierarchy process was applied to establish assessment index system and evaluation criteria, and then make a comprehensive assessment and regional difference analysis of water resources shortage risk in Sanjiang Plain. Research results showed that Shuangyashan City belonged to high degree of water resources shortage risk, while Jixi, Hegang, Jiamusi, Qitaihe, Muling and Yilan belonged to extremely high water resources shortage risk, which provided a theoretical principle for sustainable and efficient utilization of regional water resources.