In this paper, the basic concept of the reservoir submerged area is introduced. The disadvantages of two algorithms, i.e., the reservoir submerged area based on two-dimension and DEM model, and the reasons inducing errors for calculating the reservoir submerged area using this two algorithms are analyzed. Finally, an algorithm of the reservoir submerged area based on 3D GIS is presented. The basic process of calculating the reservoir submerged area using the proposed algorithm is analyzed. The feasibility in theory and the effectiveness in practice of the presented algorithm are proved.