The atom arrangement in carbon electrocatalysts is crucial for enhancing the intrinsic activity toward oxygen reduction reactions (ORRs), a key process in multiple renewable energy systems. However, the challenge of designing electrocatalysts with improved performance by manipulating atomic arrangement has been limited by synthetic constraints and a lack of understanding of the catalytic phase formation. Herein, we gain atomic-level insight into the origin of a highly active site by creating a model catalyst with a heteroatom-decorated carbon matrix of a specific configuration. The introduction of fluorine (F) during the synthesis of the nitrogen (N)-decorated carbon matrix induces structural rearrangement, converting most pyrrolic-N (Pr-N) into highly stable graphitic-N (G-N), thereby achieving a N configuration predominantly composed of pyridinic nitrogen (Py-N) and G-N. The multidopant synergistic effect of F, Py-N, and G-N causes a destabilized π-conjugated electron network of the carbon matrix, resulting in a more localized electronic structure. As a result, multiple dopant configurations with high ORR activity have been explored, among which the asymmetric Py-N and G-N configurations feature the lowest theoretical ORR overpotential, ultimately enabling the optimized F@NC catalyst to exhibit excellent oxygen reduction activity. This work establishes a foundation for the rational design of metal-free carbon-based electrocatalysts toward ORR.