Designing a structurally stable anode with a high reversible capacity for sodium ion batteries (SIBs) is particularly crucial so that batteries are able to meet the requirements for large-scale applications in grid electrical energy storage. Polyaromatic hydrocarbons (PAHs) are organic molecules with well-defined structures that demonstrate excellent performance in lithium storage. Based on our well-established correlation between battery property and molecular structure, for the first time, we applied a recently synthesized hexabenzocoronene (HBC) and corresponding derivate HBC–OMe to engage in sodium storage. The HBC molecule forms self-assemblies with a long-range ordered face-center cubed (fcc) structure due to the interaction between two HBC moieties. Such a unique 3D structure is expected to generate a strong π–π interaction between flakes and thus yield amazing durability during the long-term cycling process. In addition, the surface-dominated Na+ storage mechanism can facilitate the Na+ transport kinetics and simultaneously alleviate the structural strain during charging–discharging cycles. Benefiting from the coupling effect of the surface-driven capacitive process and the robust 3D self-assembled hierarchical nature, an oxygen-containing sample, HBC–OMe, exhibited an extraordinary sodium storage capability, attaining a high capacity of 506 mA h g−1 at 0.1 A g−1 with excellent rate capability (217 mA h g−1 at 5 A g−1) and superior long-term cycling performance (290 mA h g−1 at 2 A g−1 with negligible capacity fade after 1000 cycles).