This paper presents a robust 3D model hashing dependent on key and parameter by using heat kernel signature (HKS), which is special shape feature descriptor, In the proposed hashing, we calculate HKS coefficients of local and global time scales from eigenvalue and eigenvector of Mesh Laplace operator and cluster pairs of HKS coefficients to 2D square cells and calculate feature coefficients by the distance weights of pairs of HKS coefficients on each cell. Then we generate the binary hash through binarizing the intermediate hash that is the combination of the feature coefficients and the random coefficients. In our experiment, we evaluated the robustness against geometrical and topological attacks and the uniqueness of key and model and also evaluated the model space by estimating the attack intensity that can authenticate 3D model. Experimental results verified that the proposed scheme has more the improved performance than the conventional hashing on the robustness, uniqueness, model space.