The efficient and prompt mixing of fuel is crucial in the operation of scramjet engines. This paper presents the findings from wind tunnel experiments that examined the influence of plasma energy deposition on transverse jets at a Mach number of 6.13. The study took into account various inlet flow total pressures and momentum flux ratios between the jet and the main flow. Utilizing a database containing time-resolved intensities from instantaneous schlieren images, we perform turbulence analysis employing various techniques such as the root mean square, fast Fourier transform, proper orthogonal decomposition, and the two-point correlation method. Specifically, we aim to compare and analyze the pulsation characteristics and spatial self-organization of the jet flow field, both with and without energy deposition control. The findings reveal that intermittent “hot bubbles” created by plasma energy deposition interact with the bow shock induced by the jet, resulting in the formation of an array of large-scale vortices. These vortices emerge as the dominant structures within the jet, effectively amplifying its pulsations. At low inlet flow pressures, energy deposition primarily disrupts the jet, causing large-scale vortices to propagate primarily within the jet plume region. However, at high inlet flow pressures, the impact of energy deposition extends to both the jet and the turbulent boundary layer, encompassing their respective disturbance ranges. Increasing the inlet flow pressure constraints the evolution of large-scale vortices, thus limiting the efficacy of energy deposition in governing the mixing process.