Effects of combustion mode and cavity flame-holder on dual-mode scramjet performance were investigated using a two-dimensional computational framework developed from commercial finite element software. The objectives were to simulate the experimental data from a laboratory model scramjet with mixing enhancement device, provide better understanding of the physical processes, and to analyze the quantitative effects on the potential performance. The isolator flow field was modeled separately to match the experimentally obtained pressure rise during the Mach 2.1 isolator entry condition. The combustor heat release distribution was systematically adjusted to reproduce the wall pressure distributions from the experiments. Case studies were conducted with and without the presence of the wall cavity for scramjet operation under both thermally-choked and supersonic-combustion mode. The combustion mode affected potential tradeoffs between thrust increase and higher thermal protection need. The presence of the cavity dampened the extent of the tradeoffs by reducing the temperature change.