Semi-hydrogenation of alkynes to prepare alkenes is an important reaction in the petrochemical and fine chemical industries. The use of conventional Pd nanoparticle-based catalysts is limited by alkyne over-hydrogenation and low Pd utilization. In this study, a nitrogen-doped mesoporous carbon material (m-NC), which was rich in defect sites after Zn volatilization, was fabricated by the carbonization of ZIF-8. Ultrafine PdCo bimetallic nanoclusters with Co atom-modified Pd active site electronic and compositional structure were highly dispersed and confined in m-NC. As-obtained Pd0.43Co1/m-NC was used for the semi-hydrogenation of alkynes and it exhibited high selectivity with high conversion under mild reaction conditions. Pd0.43Co1/m-NC also exhibited excellent stability in leaching tests and maintained its catalytic activity for at least nine reaction cycles. The highly dispersed active sites in Pd0.43Co1/m-NC served as the active sites for the catalytic semi-hydrogenation of alkynes; as a regulator, the second metal Co effectively improved selectivity, and m-NC endowed the catalyst with excellent stability. The research work presented here may provide a foundation for the design of highly active, selective, and stable Pd-based bimetallic catalysts for selective hydrogenation.