With the rapid development of high-speed aircraft, the demanding for light, strong, reliable and high temperature resistive thermal protection material (TPM) is becoming urgent. High temperature material interface, such as silicon carbide (SiC) ceramic matrix composite, has received strong interest recently due to its high mechanical and thermochemical stability. For reactive interface development with nano-roughness under extremely hyperthermal non-equilibrium flow conditions for TPM applications, however, has not been reported yet. This work performs a systematic reactive molecular dynamics (RMD) study of the SiC surface morphology effect withstanding hyperthermal atomic oxygen (AO) impact via a gas–solid interface reaction model. The results show that a self-healing trend of the defect-rich silicon carbide surface with original nano-roughness is revealed towards a flatter interface accompanying with the oxidation process. The surface catalytic recombination coefficient is more sensitivity to the surface defects when wall temperature Tw > 500 K. Nano-roughness structure can also vary the main thermochemical reaction path at the thermochemical reactive interface: For the nano-groove surface model, the thermal oxidation reaction becomes dominant, while more pronounced surface catalytic recombination characteristics are revealed for the flat surface model. The mechanisms of roughness effect, surface temperature and gas impacting angle on the surface catalytic recombination, surface oxidation, and interface evolution are revealed, which advance our microscopic understanding of SiC interfacial performance with nano-roughness under non-equilibrium flow conditions.