Hard carbon (HC) anodes have shown extraordinary promise for sodium‐ion batteries, but are limited to their poor initial coulombic efficiency (ICE) and low practical specific capacity due to the large amount of defects. These defects with oxygen containing groups cause irreversible sites for Na+ ions. Highly graphited carbon decreases defects, while potentially blocking diffusion paths of Na+ ions. Therefore, molecular‐level control of graphitization of hard carbon with open accessible channels for Na+ ions is key to achieve high‐performance hard carbon. Moreover, it is challenging to design a conventional method to obtain HCs with both high ICE and capacity. Herein, a universal strategy is developed as manganese ions‐assisted catalytic carbonization to precisely tune graphitization degree, eliminate defects, and maintain effective Na+ ions paths. The as‐prepared hard carbon has a high ICE of 92.05% and excellent cycling performance. Simultaneously, a sodium storage mechanism of “adsorption‐intercalation‐pore filling‐sodium cluster formation” is proposed, and a clear description given of the boundaries of the pore structure and the specific dynamic process of pore filling. Molecular‐level control of graphitization of hard carbon (HC) with open accessible channels for sodium ions by using manganese ions, is a novel strategy to obtain HC with both high capacity and high initial Coulombic efficiency (ICE). The as‐prepared hard carbon exhibits a high ICE of 92.05% and high reversible capacity (336.8 mAh g−1).