The NDIF method based on a sub-domain technique is introduced to extract highly accurate natural frequencies of arbitrarily shaped plates with the simply-supported boundary condition. The NDIF method, which was developed by the authors for the eigen-mode analysis of arbitrarily shaped plates with various boundary conditions, has the feature that it yields highly accurate natural frequencies thanks to its effective theoretical formulation, compared with other analytical methods or numerical methods(FEM and BEM). However, the NDIF method has the weak point that it can be applicable for only convex plates. It was revealed that the NDIF method offers very inaccurate natural frequencies or no solution for concave cavities. To overcome the weak point, the paper proposes the sub-domain method of dividing a concave plate into several convex domains. Finally, the validity of the proposed method is verified in various case studies, which indicate that natural frequencies obtained by the proposed method are very accurate compared to the exact method and FEM(ANSYS).