<p>The low-voltage plateau capacity, which is highly related to the internal closed pores in hard carbon (HC), is the main contributor to the total capacity in sodium-ion batteries. However, the formation mechanism of closed pores and modification strategies at the molecular level in HC polymer precursors remain poorly understood. Furthermore, the practical applications of HCs are significantly impeded by their low initial coulombic efficiency (ICE). In this study, the intramolecular heteroatom doping (IHP) effect was proposed to facilitate the formation of closed pores in polymer-derived HC for the first time by grafting sulfonyl, ether, and carbonyl groups between benzene rings. As a result, the optimized HC sample showed an increased closed pore volume and low Na⁺ adsorption energy, which delivered a reversible capacity of 307.9 mAh·g⁻¹ and superior rate capability. Through further optimized presodiation, the formed presodiated HC featuring a thin, smooth, and dense solid electrolyte interface film exhibited a remarkably enhanced ICE of 94.4% and enhanced cycling stability (93.6% over 3000 cycles). This study provides an in-depth understanding of the formation mechanisms of closed pores <i>via</i> IHP engineering and develops a new synergistic strategy involving presodiation to prepare highly stable HC anodes.</p>