Admittedly, the surface atomic structure of heterogenous catalysts toward the electrochemical oxygen reduction reaction (ORR) are accepted as the important features that can tune catalytic activity and even catalytic pathway. Herein, a surface engineering strategy to controllably synthesize a carbon-layer-wrapped cobalt-catalyst from 2D cobalt-based metal-organic frameworks is elaborately demonstrated. Combined with synchrotron radiation X-ray photoelectron spectroscopy, the soft X-ray absorption near-edge structure results confirmed that rich covalent interfacial CoNC bonds are efficiently formed between cobalt nanoparticles and wrapped carbon-layers during the polydopamine-assisted pyrolysis process. The X-ray absorption fine structure and corresponding extended X-ray absorption fine structure spectra further reveal that the wrapped cobalt with Co-N coordinations shows distinct surface distortion and atomic environmental change of Co-based active sites. In contrast to the control sample without coating layers, the 800 °C-annealed cobalt catalyst with N-doped carbon layers enwrapping achieves significantly enhanced ORR activity with onset and half-wave potentials of 0.923 and 0.816 V (vs reversible hydrogen electrode), highlighting the important correlation between surface atomic structure and catalytic property.