Atomically-dispersed transition-metal nitrogen–carbon catalysts with specific coordination structures are promising cheap candidates for efficient oxygen reduction reaction (ORR) in metal–air and fuel cells. Nevertheless, a large part of internal active sites in this class of catalysts cannot really take effect, and the density of surface active sites is seriously insufficient. Here, a reasonable surface-host stepwise method involving adsorption and pyrolysis was designed to prepare Co–Nx/CNC electrocatalysts with highly-dispersed surface active sites, and to stabilize the isolated atomically dispersed Co–NX sites on the surface of graphitized N-doped carbon (NC). The new catalysts achieved admirable ORR activity with half-wave potential (E1/2) of 0.88 V under alkalinity. Moreover, Co–Nx/CNC showed stronger four-electron transfer ability and much higher stability. The main reason was that the coordination environment and density of active sites were effectively optimized, enabling the improvement of surface active sites and reactivity. This work provides a general approach to design and prepare highly-stabilized and abundant atomically-dispersed surface active sites for production in electrochemical energy devices.