The micro-mechanism of the silicon-based waveguide surface smoothing is investigated systematically to explore the effects of silicon-hydrogen bonds on high-temperature hydrogen annealing waveguides. The effect of siliconhydrogen bonds on the surface migration movement of silicon atoms and the waveguide surface topography are revealed. The micro-migration from an upper state to a lower state of silicon atoms is driven by siliconhydrogen bonding, which is the key to ameliorate the rough surface morphology of the silicon-based waveguide. The process of hydrogen annealing is experimentally validated based on the simulated parameters. The surface roughness declines from 1.523 nm to 0.461 nm.