The numerical simulation for near-continuum transitional flow region is a very challenging field of aerodynamics. We first introduce the NavierStokes (NS) resolver and the direct simulation Monte Carlo (DSMC) method, based on which we propose an N-S/DSMC coupling numerical algorithm by developing the modular particle-continuum (MPC) technique. This extends the application range of the DSMC method and the N-S method to the transitional flow region. Then, we explain fully the multi-level parallel optimization techniques of the coupling algorithm  on the 100P supercomputers in the National Supercomputing Center in Wuxi, and the many-core parallelization is realized for the first time. The tests show that the process-level optimization can obtain super-linear speedup. Though the many-core level optimization does not obtain the expected effect due to the features of the original algorithm and the computer architecture, we make in-depth discussion and analysis. Our research and analysis provide a reference for many-core parallelization of the coupling N-S/DSMC algorithm, and provide an effective approach for the numerical simulations of hypersonic aerodynamics.