Atomically dispersed M-N-C (M refers to transition metals) materials represent the most promising catalyst alternatives to the precious metal Pt for the electrochemical reduction of oxygen (ORR), yet the genuine active sites in M-N-C remain elusive. Here, we develop a two-step approach to fabricate Cu-N-C single-atom catalysts with a uniform and well-defined Cu2+-N4 structure that exhibits comparable activity and superior durability in comparison to Pt/C. By combining operando X-ray absorption spectroscopy with theoretical calculations, we unambiguously identify the dynamic evolution of Cu-N4 to Cu-N3 and further to HO-Cu-N2 under ORR working conditions, which concurrently occurs with reduction of Cu2+ to Cu+ and is driven by the applied potential. The increase in the Cu+/Cu2+ ratio with the reduced potential indicates that the low-coordinated Cu+-N3 is the real active site, which is further supported by DFT calculations showing the lower free energy in each elemental step of the ORR on Cu+-N3 than on Cu2+-N4. These findings provide a new understanding of the dynamic electrochemistry on M-N-C catalysts and may guide the design of more efficient low-cost catalysts.