The rational construction of non-precious metals with carbonaceous material has attracted tremendous research attention with the aim to reduce the plethoric cost of platinum for catalyzing the oxygen reduction reaction (ORR). Herein, we synthesized a highly hierarchical nanostructure framework containing metal-carbon nanotubes anchored in metal embedded porous carbon spheres (M-CNTFs) and found it has similar ORR performance to that of commercial Pt-based electrocatalysts. Based on the unique hierarchical architecture, an effective platform was constructed to explore physic-chemical insights while providing guidance to search high-efficient ORR catalysts. Electrochemical measurements show that Co-CNTFs, Fe3C-CNTFs, and Ni-CNTFs prefer to proceed through a 4e- pathway, 2e- and 4e- mixed pathways, and a 2e- pathway, respectively. Furthermore, Co-CNTFs were found to perform better than a commercial Pt-based electrocatalyst in ORR due to its lower overpotential, excellent methanol tolerance, and superior durability. In order to understand the effects of different transition metal centers on the electrocatalytic performance of M-CNTFs, corresponding calculations were performed based on the density functional theory (DFT). Results reveal that the metal active sites and hydrophilic property of the metal-carbon system play an important role in enhancing the electrocatalytic ability, which is significant for further research on (or synthesis of) excellent catalytic materials for ORR.