Sodium-ion batteries (SIBs) are attractive alternatives to lithium-ion batteries owing to their comparable performance, improved safety, and reduced reliance on critical raw materials. Hard carbon (HC) is widely regarded as the most practical anode for SIBs; however, conventional HCs still suffer from limited reversible capacity, poor rate capability, and an incompletely understood Na+ storage mechanism. Here, we investigate hazelnut shell–derived HC synthesized via a sustainable water-washing route, with a particular focus on the effects of particle size and pyrolysis temperature on electrochemical behavior. We demonstrate that smaller particle sizes improve reversible capacity and cycling stability, while uniformly distributed nanoscale inorganic impurities regulate the evolution of pore structure in HC, thereby enhancing Na⁺ storage. A clear thermodynamic relationship between the sloping and plateau capacities is identified. Operando X-ray diffraction and ex-situ Raman spectroscopy reveal that Na$^+$ storage proceeds through chemisorption in the sloping region and diffusioncontrolled Na clustering within pseudographitic domains in the low-voltage plateau, accompanied by reversible structural disordering. Density functional theory and molecular dynamics simulations further confirm that Na$^+$ preferentially chemisorbs at disordered carbon layers at higher potentials and subsequently forms semimetallic Na clusters within nanopores adjacent to pseudographitic layers at lower potentials, closely linked to the pre-adsorbed Na$^+$ species. These findings provide fundamental mechanistic insight into Na$^+$ storage in biomass-derived HC and offer clear guidelines for optimizing HC anodes toward high-performance SIBs.