Enlarging the M-Nx active-site density is an effective route to enhance the ORR performance of M-N-C catalysts. In this work, a single-atom catalyst Cu–N@Cu–N–C with enlarged Cu–N4 active site density was prepared by the second doping and pyrolysis (SDP) of Cu–N–C derived from Cu-doped zeolite imidazole frameworks. The half-wave potentials of Cu–N@Cu–N–C were measured as 0.85 V in alkaline electrolyte and 0.75 V in acidic media, which was 50 mV and 60 mV higher than that of Cu–N–C, respectively. N2 adsorption–desorption isotherm curves and corresponding pore distribution analysis were used to verify the successful filling of additional Cu and N in micropores of Cu–N–C after SDP. The obvious increase in Cu contents for Cu–N@Cu–N–C (1.92 wt%) compared with Cu–N–C (0.88 wt%) tested by ICP demonstrated the successful doping of Cu into Cu–N–C. XAFS analysis confirmed the presence of Cu–N4 single-atom active centers in Cu–N@Cu–N–C. The N 1 s high-resolution XPS results proved a great increase in Cu–N4 contents from 13.15% for Cu–N–C to 18.36% for Cu–N@Cu–N–C. The enhanced ORR performance of Cu–N@Cu–N–C was attributed to the enlargement of Cu–N4 active site density, providing an effective route for the preparation of efficient and low-cost ORR catalysts.