In this study, insights into the sodium storage mechanisms for different states of sodiation are obtained from X-ray total scattering measurements on three representative HCs with distinct microstructures. Subsequently, the local configurational states are evaluated by density functional theory (DFT) to provide atomic-level insights into the enthalpies and feasibility of sodium interactions within the HC structures. We find that HC microstructures prepared at higher pyrolysis temperatures, which exhibit larger average pore sizes, facilitate the formation of larger sodium clusters, thereby increasing capacity through sodium storage in the pores. Furthermore, we infer that initial irreversibility primarily arises from sodium adsorption at high-binding energy surface defect sites, resulting in trapped sodium, and the formation of a solid electrolyte interface (SEI).