Atomically dispersed catalysts have gained considerable attention due to their unique properties and high efficiency in various catalytic reactions. Herein, a series of Co/N-doped carbon (N-C) catalysts was prepared using a metal-lignin coordination strategy and employed in formic acid dehydrogenation (FAD) and hydrodeoxygenation (HDO) of vanillin. The atomically dispersed Co/N-C catalysts showed outstanding activity, acid resistance, and long-term stability in FAD. The improved activity and stability may be attributed to the high dispersion of Co species, increased surface area, and strong Co-N interactions. XPS and XAS characterization revealed the formation of Co-N3 centers, which are assumed to be the active sites. In addition, DFT calculations demonstrated that the adsorption of formic acid on single-atom Co was stronger than that on Co13 clusters, which may explain the high catalytic activity. The Co/N-C catalyst also showed promising performance in the transfer HDO of vanillin with formic acid, without any external additional molecular H2.