A modified NDIF method using a sub-domain approach is introduced to extract highly accurate eigenvalues of two-dimensional, arbitrarily shaped acoustic cavities. The NDIF method, which was developed by the authors for the eigen-mode analysis of arbitrarily shaped acoustic cavities, has the feature that it yields highly accurate eigenvalues 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 cavities. It was revealed that the solution of the NDIF method is very inaccurate or is not suitable for concave cavities. To overcome the weak point, the paper proposes the sub-domain method of dividing a concave domain into several convex domains. Finally, the validity of the proposed method is verified in two case studies, which indicate that eigenvalues obtained by the proposed method are more accurate compared to the exact method, the NDIF method, or FEM(ANSYS).