The staged injection scheme has drawn an increasing attention for the airbreathing hypersonic propulsion system, and the fuel injection angle has a large impact on the mixing improvement between the fuel and the supersonic cross flow. The Reynolds-averaged Navier–Stokes equations associated with the SST k-ω turbulence model have been employed to investigate the interaction mechanism in the staged sonic injection flow field, and the influences of the injection angle, the injection angle arrangement, and the distance between the injectors on the flow field characteristics have been analyzed comprehensively. At the same time, three grid scales have been used to perform the grid independency analysis, and the predicted results have been compared with the experimental data in the open literature for the single transverse injection scheme. The obtained results show that the penetration height for the cases with the distance between the injectors being 1 mm is the highest in the range considered in the current study, and this may be due to the strongest shock wave/shock wave interaction between the injectors. At the same time, due to the blockage of the fuel injection, the penetration height increases as the supersonic air stream flows downstream, and the influence of the wave system generated by the first and third injectors cannot propagate downstream and upstream, respectively. The multi-port injection scheme can provide better fuel penetration performance than the single one when the flow flux keeps constant, and the multi-port injection scheme with a certain angle can provide a higher total pressure recovery efficiency than the staged transverse injection scheme. Further, the staged transverse injection flow field can provide a better recirculation zone for the mixing between the fuel jet and the boundary layer, and the separation length increases with the increase of the distance between the injectors.