Supersonic incoming flow has a large momentum, which makes it difficult for transverse jets to have a large penetration depth due to the strong compression of the incoming flow. This impacts the mixing efficiency of the jet in the supersonic combustor. This paper proposes a method to improve the mixing efficiency of a rectangular flow field model using pulsed energy deposition, which is verified numerically. In the simulations, the Navier−Stokes equations with an energy source are solved to simulate the effects of energy deposition with various distributions on the fuel mixture. The results show that the energy deposition increases the turbulent kinetic energy, which enlarges the scale of the flow vortex and improves the fuel mixing performance. The energy deposition is distributed upstream and significantly improves the mixing performance. Energy deposition can improve the penetration depth of fuel, which is more significant when the energy deposition is distributed downstream of the jet orifice. The energy deposition also slightly reduces the total pressure recovery coefficient. In general, an energy deposition that is distributed upstream of the jet has the best effect on the mixing efficiency.