The optimization of carbon-based multi-scale structures including morphology, crystallinity and doping functionality has been demonstrated effective in enhancing the anodic properties for sodium ion batteries. A one-step regulation strategy of these multi-scale structures is still highly desirable. Herein, we report a simple boron doping strategy to achieve simultaneous optimization of carbon-based multi-scale structures including spherical morphology, crystalline parameters and boron doping environment to enable enhanced Na⁺ storage properties and high-performance full-cell sodium ion batteries. The carbon synthesis is achieved by a hydrogen bond guided co-assembly process followed by high-temperature carbonization with boric acid and glucose as boron and carbon sources, respectively, which endows the obtained boron-doped hard carbon nanospheres with a polydisperse nanosphere morphology, specific boron species (BC₃ and B–C–O) and enlarged interlayer distance. These structural merits collectively enable the improved Na⁺ storage capacity and rate capability. In particular, the plateau capacity of the boron doped carbon anode increases by 67% as compared with the non-doped carbon anode; especially, the intercalation capacity increases by nearly 3 times. Density functional theory calculations for the first time reveal the enhanced Na⁺ diffusion and insertion dynamics within the boron doped carbon interlayer, which explains the greatly boosted intercalation capacity. Furthermore, the galvanostatic intermittent titration technique (GITT) and operando measurement collectively demonstrated that the boron doped carbon anode promotes the diffusion dynamics of Na⁺ between microcrystalline interlayers, hence facilitating a diffusion-controlled Na⁺ insertion process. The constructed full-cell exhibits a high energy density of 244.6 W h kg⁻¹ and an excellent cycling stability, implying the application potential of the boron doped hard carbon spheres in sodium ion batteries.