A transverse jet in the supersonic crossflow is one of the most promising injection schemes in scramjet, where the control or enhancement of jet mixing is a critical issue. In this paper, the effect of the backward facing step on the characteristics of jet mixing was investigated by three-dimensional large eddy simulation (LES). The simulation in the flat plate configuration (step height of 0) was performed as the baseline case to verify the computation framework. The distribution of the velocity and pressure obtained by the LES agreed well with the experiment, which shows the reliability of the LES code. Then, two steps with a height of 1.0D and 1.58D (D is the injector diameter) were numerically compared to the non-step baseline case. The comparison of the three cases illustrates the effect of the large-scale recirculation region on the variable distribution, and shock and vortex structures in the flow field. In the windward region, the shear layers become thicker, and the convection velocity of the shear vortexes reduces. In the leeward region, the wake vortices almost disappear while the counterrotating vortex pairs (CVPs) expand in the spanwise direction. In the area upstream of the jet, the separation bubble works with the upstream large-scale recirculation zone to entrain the jet into the upstream near-wall zone. At last, a comparison of the overall mixing performance of the three cases revealed that the penetration depth and mixing efficiency increased with the step height increasing.