The inherent catalytic activity of transition metal oxide catalysts is constrained by the presence of surface hydroxyl groups, which are typical destructive poisons that are difficult to be completely removed. So, previous studies generally focused on reducing the accumulation of hydroxyl groups on the surface by introducing additional elements. In this study, a simple reflux treatment in methanol considerably increases the CO oxidation activity, water resistance, and stability of Co3O4. According to the density functional theory calculations, the cleaning of hydroxyl groups by methanol is spontaneous, and the assembled methanol has little effect on the surface chemical properties. In addition, the molecular dynamics simulations indicate that methanol molecules have formed hydrophobic entrances in the pores of Co3O4, which further protect the internal surface from erosion by water. Furthermore, methanol functionalization maintains the original CO oxidation mechanism on the clean Co3O4 surface. As a result, the inherent catalytic activity of Co3O4 is awakened while the water resistance and stability are improved. Collectively, this study establishes an atomic‐level description for the surface cleaning and protection mechanism on Co3O4 surface through functionalization by small organic molecules, which provides a new theoretical guidance for the modification strategies of transition metal oxide catalysts.