Biomass is the most abundant renewable resource on earth and developing high-performance nonprecious selective hydrogenation (SH) catalysts will enable the use of biomass to replace rapidly diminishing fossil resources. This work utilizes ZIF-67-derived nitrogen-doped carbon nanotubes to confine Co nanoparticles (NPs) with Co-N-x active sites as a high-performance SH catalyst. The confined Co NPs with Co-N-x exhibit excellent catalytic activity, selectivity, and stability toward a wide range of biomass-derived compounds. Such active sites can selectively hydrogenate aldehyde, ketone, carboxyl, and nitro groups of biomass-derived compounds into value-added fine chemicals with 100% selectivity. The reported approach could be adopted to create other forms of catalytically active sites from other nonprecious metals.