Understanding and predicting how heteroatomic dopants of carbon nanotubes (CNTs)-based catalysts alter their catalytic performance at nanoscale is essential to design superior electrocatalysts for oxygen reduction reaction (ORR). This report describes findings of an investigation of the heteroatomic dopant-activity relationship for Co3O4/doped CNTs catalysts with different heteroatoms including N, O, and P atoms in ORR. By using an array of techniques to probe the structure and elementary valence of the catalysts, the incorporation of the Co3O4 nanoparticles can introduce defects into the doped CNTs, especially the N-CNTs, which should contribute to the generation of active sites. The Co3O4/N-CNTs are shown to exhibit both the highest ORR activity and stability compared with Co3O4/O-CNTs, Co3O4/P-CNTs, and Co3O4/CNTs, manifesting the synergistic correlation of Co3O4 nanoparticles, heteroatoms, and CNTs. This kind of synergy is assessed by density functional theory calculations based on the electronic properties and molecular orbitals. It is found that N, O, or P atoms can tune the charge distribution of CNTs by decreasing the lowest unoccupied molecular orbital-highest occupied molecular orbital energy gap, thus activating the adjacent C atoms. And the addition of Co3O4 will further redistribute the charge of CNTs from CNTs to Co3O4 toward enhanced ORR activity. Moreover, the Co3O4/N-CNTs catalyst exhibits a maximum structural stability due to the strong electronic interaction between Co2+ ions and N atoms, which is believed to result in its high ORR stability. Analysis of the results, along with a combined theoretical and experimental study, has provided implications for the design of catalysts with controlled activity and stability for ORR.