In the present work, a general sub-domain boundary mapping procedure has been developed for arbitrary topology multi-block structured grids with grid points matched on sub-domain boundaries. The interface of two adjacent blocks is uniquely defined according to each local meshing index system (MIS) which is specified independently. A pack/unpack procedure based on the definition of the interface is developed to exchange the data in ID array to minimize the communication amount. A safe send/receive procedure is built to remove the possibility of communication block and achieve an optimum parallel computation efficiency. The procedure is applied to parallelize an in house 3D Navier-Stokes code. The message passing interface (MPI) protocol is used for the data communication. The implementation of this newly developed parallelization procedure is straightforward. The programming work to convert a sequential code to parallel code using this procedure is minimal. The numerical experiments on an MPI based computer cluster show that the general mapping algorithm is robust and has high parallel computation efficiency.