Carbon material has emerged as a highly promising anode for sodium‐ion batteries (SIBs) due to its abundance of resources, cost‐effectiveness, and high carbon yield. This work elaborately designs the precursor structure for the self‐assembly of melamine‐cyanuric acid on the anthracite surface through hydrogen bonding, and successfully constructs N‐doped carbon with tailored microstructure and expanded interlayer spacing. Serving as anode for SIBs, the optimized sample delivers high specific capacity (371.3 mAh g−1 at 0.05 A g−1), superior rate capability (295.8 mAh g−1 at 10.0 A g−1), and excellent ultra‐long cycling performance (the retention of 91.5% after 3000 cycles at 0.5 A g−1). The systematic investigations reveal the enhancement of sodium‐ion storage in the low‐voltage plateau region involving the interlayer intercalation coupled with nanopores filling. It is discovered that the microporous structure formed by the appropriate graphite sheet angle influences the migration and storage of sodium ions. Density functional theory calculations indicate that the adsorption capacity for sodium ion is enhanced and the migration energy barrier perpendicular to the graphite layer is reduced at the appropriate angle of 8°. This study provides novel insights into the sodium‐ion storage mechanism, offering guidance for the better design of anthracite‐based carbon anode with superior performance.