In this study, the aerodynamic analysis of NASA Common Research Model (wing-body configuration) was conducted by a block-structured Cartesian mesh method named Building-Cube method. The building-cube method (BCM) has the advantages of the quick and robust mesh generation and efficient parallel computing, and it is easy to run on a large-scale computing system. However, the BCM suffers a restriction on the resolution of the turbulent boundary layer. The aim of this study is to improve the resolution issue of the turbulent boundary layer at high Reynolds number flows using the immersed boundary method. By utilizing the advantages of the BCM, we challenge to resolve the boundary layer by mesh subdivision. In this paper, the results of the validation before subdivision mesh were shown by using a coarse mesh. The computational results were compared with the transonic wind tunnel test and the results of another flow solver. Although the results showed a similar tendency with the results of another flow solver, the decomposed aerodynamic coefficient appeared with some discrepancy.