Abstract: To investigate the fuel injection and mixing issues in the scramjet combustor, three-dimensional multi-species compressible flow solver has been developed using high-resolution numerical schemes and SST k－ω turbulence model. Firstly, a classical experiment was applied to validate the accuracy and reliability of the code in predicting complex flow structures induced by hydrogen injection in supersonic crossflows. Then the effects of fuel injection configuration (single hole or dual holes) on the flow field and mixing performance were thoroughly investigated. The obtained results show that the developed code can accurately simulate the complex flow features and mixing characteristics induced by fuel injection in supersonic flows. For the single injection, the counter-rotating vortex pairs (CVP) and the induced tailing counter-rotating vortex pairs (TCVP) dominate the mixing process, and this physical phenomenon can also be observed in the dual injection case. The streamwise vortex distribution exhibits significant differences between the single and dual injection cases. For the dual injection case, the streamwise vortex presents more complex variations. Besides, the mixing efficiency of dual injection case is lower at the initial stage while it has better mixing performance in the downstream region.