The present computational study examines the effect of vortex height on characteristics of bow shock/vortex interaction as a practical technique for improving mixing of fuel and air in Scramjet engines. The bow shock/vortex interaction is induced through placing a vortex generator in the form of a semi-span wing section at an angle of attack upstream of a flat plate with an injection slot. The vortex interacts with the injection induced bow shock, and for a sufficiently strong interaction a supersonic vortex breakdown is expected. The results of the computational study demonstrate that reducing the vortex height leads to the interaction of the vortex with the stronger portion of the bow shock, which results in a vortex breakdown for all examined jet momentum ratios. Results indicate that moving the vortex center close to the plate surface leads to a significant destruction of the vortex core and formation of large subsonic region and a downstream displacement of the primary separation shock due to the Mach number deficit. Additionally, increased mixing of injectant with the supersonic cross flow for all examined cases is observed.