Engineering interfacial built-in electric fields (BEFs) has emerged as a powerful strategy to boost the electrochemical performance of sodium-ion batteries (SIBs), yet the controllable amplification of BEF intensity remains a long-standing challenge. Herein, we propose an anion reconfiguration strategy enabled by in situ thermodynamically driven phase transition processes to tailor heterojunction crystal structures (i.e., FexSez/CoySez). This approach enables precise regulation of Fermi-level alignment and interfacial charge redistribution, thereby achieving effective BEF modulation with a high field intensity. We further propose a theoretical framework that elucidates the role of the BEF effect in accelerating electron/ion kinetics, suppressing irreversible side reactions, and promoting the formation of the inorganic-dominated solid–electrolyte interphase. Benefiting from the strengthened BEF, the optimized Fe3Se4/CoSe2 heterojunction electrode delivers outstanding rate capability (236.8 mAh g−1 at 100 A g−1) and exceptional cycling stability, retaining ∼100% capacity over 6000 cycles at 20 A g−1, which significantly outperforms commercial hard carbon and ranks among the best reported to date. Furthermore, industrial-scale pouch cells are assembled to validate the practical feasibility of this strategy. This work broadens the understanding of BEF formation and modulation mechanisms for unlocking the full potential of high-performance SIBs.