Abstract The solid electrolyte interface (SEI) on electrode materials remains a critical challenge in the development of alkali metal‐ion batteries, with its complex formation mechanism and diverse composition significantly impacting practical performance. Herein a theory‐guided prediction approach is presented to construct a rigid–soft coupling SEI, engineered through the strategic regulation of both interfacial and bulk electrochemistry for the design of nitrogen‐ and boron‐coordinated cobalt single atoms within nitrogen‐doped carbon (Co–N₃B/C) anodes. The experimental and theoretical findings reveal that the distinctive Co–N 3 B configuration tends to generate a local electric field that benefits for fast Na + transfer kinetics and the decomposition of fluorinated electrolyte, resulting in the formation of a robust inorganic‐rich SEI. Consequently, the dual‐coordinated Co single‐atom electrode design, coupled with the hybrid organic–inorganic SEI, endows the sodium‐ion batteries anode with a high capacity of 230.5 mAh g −1 at 2 A g −1 and exceptional long‐term cycling stability, as evidenced by 97.0% capacity retention over 5000 cycles at 2 A g −1 . This study not only demonstrates the significant advantages of single‐atom catalysis in controlling SEI formation and electrolyte degradation but also paves the way for using this technology to enhance the performance of carbon‐based anodes in a wide range of metal‐ion batteries.