An extensive interest in the numerical simulation of supersonic combustion ramjet engine (scramjet) has been aroused among researchers at present. Nevertheless, the traditional serial simulation model cannot meet the requests of current researches, such as millions of computational grids and hundreds of reaction processes. In this paper, we study on a general algorithm for scramjet design, and bring about parallelization by using a two-level hybrid parallel programming model. The method includes message passing for inter-node communication (MPI) and compiler directives for intra-node parallelization (OpenMP). Finally, parallel efficiency on a China-made supercomputer with 4 to 256 cores is compared with pure MPI program. The result indicates that our hybrid parallel model is simple, effective and practical in scramjet simulation.