It is a consensus that hydrogen is the essential mobile impurity associated with the degeneration of silicon devices in ionization radiation. Specifically, it is proton that extends interfacial defects in SiO 2 /Si interface. In this work, the proton diffusion and the induced defects in the amorphous-SiO 2 /Si (a-SiO 2 /Si) interface are simulated at multi-scales. The diffusion activation energy and pre-exponential factor are obtained by fitting the Arrhenius law, and the interfacial defects associated with the proton diffusion are identified from the diffusion trajectories. Moreover, the pathways and barriers of proton migration in the a-SiO 2 /Si interface are calculated by the climbing image nudged elastic band (CI-NEB) method, which indicates a potential barrier of 0.2–0.6 eV for a proton to migrate between the bridging O atoms. Further by comparing the energy barrier profiles in the lateral and perpendicular directions, it is suggested that the proton diffusion is anisotropic in the a-SiO 2 /Si interface. A proton is more likely to migrate laterally in the first few Si layers beneath the interface, rather than crossing over the interface, and it may be trapped in the latter process due to the unevenly distributed strain in a-SiO 2 /Si interface. • Multi-scale simulations predict the anisotropic performance of hydrogen diffusion in amorphous-SiO 2 /Si interface. • The first unoxidized Si layer beneath the interface is proved to be an effective sink for hydrogen. • The diffusion-induced defects of protons are identified in terms of the trajectories via visual molecular dynamics program.