Greedy algorithm is one of the important point selection methods in the radial basis function based mesh deformation. However, in large-scale mesh, the conventional greedy selection will generate expensive time consumption and result in performance penalties. To accelerate the computational procedure of the point selection, a block iteration with parallelization method is proposed in this paper. By the block iteration method, the computational complexities of three steps in the greedy selection are all reduced from O ( n 3 ) to O ( n 2 ) . In addition, the parallelization of two steps in the greedy selection separates boundary points into sub-cores, efficiently accelerating the procedure. Specifically, three typical models of three-dimensional undulating fish, ONERA M6 wing and three-dimensional Super-cavitating Hydrofoil are taken as the test cases to validate the proposed method and the results show that it improves 17.41 times performance compared to the conventional method.