Surface and subsurface are commonly considered as separate entities because of the difference in the bonding environment and are often investigated separately due to the experimental challenges in differentiating the surface and subsurface effects. Using in-situ atomic-scale transmission electron microscopy to resolve the surface and subsurface at the same time, we show that the hydrogen-CuO surface reaction results in structural oscillations in deeper atomic layers via the cycles of ordering and disordering of oxygen vacancies in the subsurface. Together with atomistic calculations, we show that the structural oscillations in the subsurface are induced by the hydrogen oxidation-induced cyclic loss of oxygen from the oxide surface. These results demonstrate the propagation of the surface reaction dynamics into the deeper layers in inducing nonstoichiometry in the subsurface and have significant implications in modulating various chemical processes involving surface-subsurface mass transport such as heterogeneous catalysis, oxidation, corrosion and carburization.