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The structure of polyanionic materials is conventionally known to be free of transition metal migration and structurally stable when storing/releasing sodium ions. Herein, the observation of enhanced cycling stability of a typical polyanionic cathode, Na₃VCr(PO₄)₃(NVCP) at lower temperature (−15 °C vs 30 °C), triggers the exploration of its structural origins with a surprising finding that the migratable nature of vanadium in NVCP leads to detrimental structural degradation of the polyanionic host upon cycling. The correlation between long range and short range structural change associated with this atomic migration is established via a strong combination of various in situ/ex situ characterization tools, revealing the essential V–to–Na1 site migration. Such transition metal migration is effectively suppressed when V atoms are pinned to their original position in the lattice by lowering the temperature. More importantly and practically, a room temperature‐based deep sodiation strategy is further developed to recover the structure. This work challenges the long‐standing assumption of the stability of the polyanionic framework structure and calls for urgent attention to the structural understanding of the NVCP system as well as strategy development for property enhancement.