Hard carbon (HC) has been considered as promising anode material for sodium-ion batteries (SIBs). The optimization of hard carbon’s microstructure and solid electrolyte interface (SEI) property are demonstrated effective in enhancing the Na+ storage capability, however, a one-step regulation strategy to achieve simultaneous multi-scale structures optimization is highly desirable. Herein, we have systematically investigated the effects of boron doping on hard carbon’s microstructure and interface chemistry. A variety of structure characterizations show that appropriate amount of boron doping can increase the size of closed pores via rearrangement of carbon layers with improved graphitization degree, which provides more Na+ storage sites. In-situ Fourier transform infrared spectroscopy/electrochemical impedance spectroscopy (FTIR/EIS) and X-ray photoelectron spectroscopy (XPS) analysis demonstrate the presence of more BC3 and less B–C–O structures that result in enhanced ion diffusion kinetics and the formation of inorganic rich and robust SEI, which leads to facilitated charge transfer and excellent rate performance. As a result, the hard carbon anode with optimized boron doping content exhibits enhanced rate and cycling performance. In general, this work unravels the critical role of boron doping in optimizing the pore structure, interface chemistry and diffusion kinetics of hard carbon, which enables rational design of sodium-ion battery anode with enhanced Na+ storage performance.