Hydrogen plasma treatment (HPT) is commonly employed to enhance the interface quality of high-k metal-oxide gate stacks in semiconductor, but the plasma process is highly sensitive to variations in process parameters. The modulation of processing conditions to meet the increasing demand for atomic-precision in device feature is severely challenging without a proper understanding of the plasma-facing surface. This study aimed to provide atomistic insights on HPT to improve the quality of high-k metal-oxide/silicon interfaces through a computational approach via molecular dynamics and density functional theory. Hydrogen collision, adsorption, penetration, diffusion and desorption were simulated on the processed surface. Depth-wise distribution of hydrogen, structural evolution of target surface and the resultant charge traps at the interface were captured in the computational model for varying processing conditions, incident atomic energies and substrate temperatures. Notably, a physical correlation between the processing parameters and the interface quality was found; the dangling bond density is directly- (at low E) or inversely proportional (at high E) to the substrate temperature, causing variations in trap defects and stability of the gate stacks. A concrete understanding of the HPT offers a guideline to optimize the process window and development of advanced equipment for practical use.