The excess energy of subsurface hydrogen species may facilitate overcoming reaction barriers and remarkably alters the reaction pathways. We present an in-depth study on the different reactivity of surface and subsurface hydrogen species in syngas methanation on the O/C-covered Pd(100) by using density functional theory calculations and microkinetic simulations. It is shown that the apparent energy barriers to form H2O and CH4 are reduced by 0.87 and 0.61 eV for the case in which the hot subsurface hydrogen species are involved in the whole hydrogenation process. The activity of O-covered Pd(100) is better than that of the C-covered surface, and the reactivity of subsurface hydrogen species is much higher than that of surface hydrogen species under ambient conditions. Increasing CO partial pressure strongly enhances the reactivity of subsurface hydrogen species in syngas methanation on the O-covered Pd(100). These important results are helpful for understanding the hot-atom mechanism through subsurface heterogeneous catalysis.