In this study, the direct simulation Monte Carlo method was used in simulating the internal flow field and fuel mixing efficiency of a three-dimensional supersonic combustion ramjet (scramjet) engine to investigate the changes in the internal field of air inlets at varying Mach numbers and for different physical appearances. The study results show that oblique shock waves and normal shock waves affect the mixing quality of hydrogen in the combustion chamber. The simulated air inlet conditions were 12, 15, and 18 Mach. In addition, two types of physical appearances were tested, specifically, concave cavity and rear-ramped concave cavity. By comparing the results obtained from the three-dimensional simulations with extant two-dimensional simulation results, this study endeavors to increase simulation accuracy. These comparative results can then be used as a reference for conducting major simulations in the future.