A hybrid catalyst support anchoring a noble metal catalyst could be a promising material for building interfacial bonding between metallic nanostructures and polymer functionalized carbon supports to improve the kinetics of oxygen reduction reaction (ORR). This study successfully prepared a polyhedron nanostructured Pd and MoO2-embedded polyaniline-functionalized graphitized carbon nitride (PANI-g-C3N4) surface using a chemical reduction method. The Pd–Mo/PANI-g-C3N4 achieved an ORR activity of 0.27 mA µg−1 and 1.14 mA cm−2 at 0.85 V, which were 4.5 times higher than those of commercial 20% Pt/C catalyst (0.06 mA µg−1 and 0.14 mA cm−2). In addition, the Pd–Mo/PANI-g-C3N4 retained ∼ 77.5% of its initial mass activity after 10,000 cycles, with only 30 mV half-wave potential reduction. Further, the engineered potential active sites in the catalyst material verified the significant improvement in the ORR activity of the catalyst with increased life-time, and theoretical calculations revealed that the synergistic effect of the catalytic components enhanced the ORR kinetics of the active sites.