The scramjet engine burns fuel under supersonic flow condition in a combustion chamber while minimizing total pressure such that it can operate under both supersonic and hypersonic flows. For combustion under supersonic flow field, a flame holder is essential to overcome short fuel residence time and poor mixing, and a backward facing step is the simplest and best performing method that can be used as a flame holder. Proper interaction between the flame holder and fuel injection can improve engine performance in fluidic conditions. However, it creates significantly more heating condition that imposes challenges in thermal design and thermal management. In the flame holder design, measuring and analyzing the flow mixing and heat transfer characteristics should be preceded. In this study, flow mixing and heat transfer characteristics analysis by flame holder and secondary injection were performed by numerical simulations. In a flow field with Mach 3 mainstream, the test domain in which a 5 mm backward facing step and a hole for fuel injection in the downstream area was selected for experiment. The sonic jet is generated in the circular hole. First, to analyze the effect of the backward facing step on the secondary injection and supersonic crossflow, heat transfer and comparative analyses were performed with and without the backward facing step. And the effect of the ratio between hole position and step height on the heat transfer was analyzed. Two approaches were used to analyze the heat transfer. One was to analyze the point where the transfer phenomenon increased, and the second was to analyze how much the area affected as the heat transfer increased. As the position of the hole on the step raised, the resulting heat transfer increased, but the area size affected by this high heat transfer decreased and then increased again.