This paper reports a systematic computational investigation that elucidates the fundamental thermochemical non-equilibrium physics that occurs when air at Mach number of 11 encounters a rectangular cavity of aspect ratio L/D = 2.0 embedded on a 25° compression ramp. The mechanistic details of this highly complex flow phenomenon are obtained by solving the compressible form of the Navier–Stokes equations in two dimensions using a finite-volume open-source library. Chemical and thermal non-equilibrium processes are treated using a five-species, 12-reaction chemical kinetics, and a two-temperature model, respectively. Following a detailed validation and grid sensitivity study, two simulations are conducted, one with isothermal boundary conditions and the other with conjugate heat transfer (CHT) to identify the effect of energy transmission to the material on surface heat flux. Fast Fourier transforms and near-wall velocity profiles inside and in the neighborhood of the cavity are used to identify primary oscillatory modes and shear layer dynamics. Two new descriptive states defined as “states I and II,” representative of the minimum and maximum deflection of the shear layer, are used to discuss the dynamical behaviors in the cavity, including the separation region before the cavity, trailing edge effects, frequency analysis of probe data collected at several key locations, and the effect of CHT on surface heat flux. It is found that the flow features at the cavity's center strongly influence the separation upstream of the cavity, and the transrotational temperature near the cavity's trailing edge is strongly correlated with the oscillations of the shear layer.