Dual-doping of carbon, especially the combination of nitrogen and a secondary heteroatom, has been demonstrated efficient to optimize the oxygen reduction reaction (ORR) performance. However, the optimum dual-doping is still not clear due to the lack of strong experimental proofs, which rely on a reliable method to prepare carbon materials that can rule out the interference factors and then emphasize only the doping effects. In this work, an inside-out doping method is reported to prepare carbon submicrotubes (CSTs) as a material to study the principles of designing dual-doping catalysts for ORR. The interference factors including the metal impurities and doping gradient in the bulk phase are excluded, and the doping effects including the structural and chemical variation of carbon are studied. P-doping exhibited a higher pore-forming ability to perforate carbon and a lower doping content, but a higher ORR catalytic activity as compared with S- and B-doped N-CSTs, demonstrating the N, P co-doping is more efficient in making carbon-based catalysts for ORR. First-principle calculations reveal that the edge C situated around the oxidized P site nearby a graphitic N atom is the active site that shows the lowest ORR overpotential comparable to Pt-based catalysts. This study suggests that the catalytic activity of dual-heteroatoms-doped carbons not only depends on the intrinsic chemical bonding between heteroatoms and carbon, but also is affected by the structural variation generated by introducing different atoms, which can be extended to the study of other kinds of functionalization of carbon and potential reactions besides ORR.