Recognization of the dynamic evolution of the catalytic active site and battery reaction intermediates under working conditions is essential for optimal design of advanced electrocatalysts for lithium–oxygen batteries, yet remaining formidable challenges because of size, carrier, and surface interface effect on traditional supported catalysts. Herein, based on the designed single-Co-atom catalyst model with uniform and isolated active centers, the structural dynamic evolution of near-free active centers and the complicated reaction pathways of lithium–oxygen electrochemistry is firstly in-depth identified at the atomic level by virtue of structural and ingredient measurements at multiscale levels. We discover that the near-free Co site (Co1-N3) tends to be dynamically released from the nitrogen-carbon substrate, and then forms a freer O*-Co1-N2 site, facilitating the surface adsorption and activation of the key *O intermediate for oxygen reduction reaction during discharge. More interestingly, near-free Co exists a better lattice match with the (100) crystal plane of Li2O2, forming an easily decomposed single-oriented sheet-like Li2O2 with higher electron transport capacity and weaker *LiO2 combination, thus improving the kinetics of oxygen evolution reaction during recharge. The integration of multiple test techniques on single-atom catalyst model in this study may pave the way for revealing important dynamic evolution steps and reaction mechanisms at three-phase boundaries in metal–air batteries.