ABSTRACT Aqueous magnesium‐ion batteries (AMIBs) have emerged as promising energy storage systems owing to their intrinsic safety, high energy density, and cost‐effectiveness. However, the intercalation of high‐charge‐density Mg 2+ usually leads to irreversible structural degradation toward conventional electrodes with low practical capacity and inferior stability. To overcome the inherent lattice stress caused by Mg‐ion, we investigated a series of flexible organic molecules (FOMs), and for the first time proposed a novel ion‐adaptive strategy, achieving a high‐performance FOM with modulated molecular steric hindrance, high practical capacity, and robust stability in AMIBs. In contrast with ever‐increasing lattice stress with successive Mg‐ion intercalation in conventional electrode, the subsequent ion intercalation reduced the stress by facilitated ion‐storage in the optimized ion‐adaptive FOM, such as tribenzoquinoxaline‐5,10‐dione (3BQ), with ultimately improved practical capacity (332.1 mAh g −1 at 1.0 A g −1 ), ranking among the highest capacity in AMIBs to date. Furthermore, the expanded planar architecture confers enhanced cycling stability on the ion‐adaptive 3BQ, maintaining a high specific capacity of 196.7 mAh g −1 even after 7,000 cycles at 10.0 A g −1 . The novel ion‐adaptive strategy provides a new pathway to design high‐capacity electrode materials in AMIBs and other multivalent‐ion batteries.