The non-equilibrium chemical reacting combustion flows of a proposed long slender scramjet system were numerically studied by solving the turbulent Reynolds averaged Navier-Stokes (RANS) equations. The Spalart-Allmaras one equation turbulence model is used which produces better results for near wall and boundary layer flow field problems. The lower-upper symmetric Gauss-Seidel implicit scheme, which enables results converge efficiently under steady state condition, is combined with the weighted essentially non-oscillatory (WENO) scheme to yield an accurate simulation tool for scramjet combustion flow field analysis. Using the WENO schemes high-order accuracy and its non-oscillatory solution at flow discontinuities, better resolution of the hypersonic flow problems involving complex shock-shock/shock-boundary layer interactions inside the flow path, can be achieved. Two types of scramjet combustor with cavity-based and strut-based fuel injector were considered as the testing models. The flow characteristics with and without combustion reactions of the two types of combustor models were studied with a transient hydrogen/oxygen combustion model. The detailed results of aerodynamic data are obtained and discussed, moreover, the combustion properties of varying the equivalent ratio of hydrogen, including the concentration of reacting species, hydrogen and oxygen, and the reacting products, water, are demonstrated to study the combustion process and performance of the combustor. The comparisons of flow field structures, pressure on wall and velocity profiles between the experimental data and the solutions of the present algorithms, showed qualitatively as well as the quantitatively in good agreement, and validated the adequacy of the present simulation tool for hypersonic scramjet reacting flow analysis.