Rechargeable calcium-ion batteries have become intriguing alternatives for grid-scale energy storage devices. However, the strong electrostatic interaction caused by the intrinsic divalent nature of Ca2+ leads to sluggish ion diffusion kinetics, thus resulting in low capacity. Herein, a small molecular crystal organic material is employed as the electrode material for the aqueous calcium-ion batteries. This kind of organic material could not only bypass the sluggish ion diffusion through carbonyl enolization but also avoid electrode inevitable dissolution due to the intermolecular hydrogen bonding, and flexible structure. In addition, the robust crystal structure allows fast Ca-ion diffusion and storage. Electrochemical characterization including electrochemical quartz crystal microbalance combined with first-principles density calculations and in(ex)-situ spectroscopy methods reveals the whole Ca-ion storage mechanism at the atomistic and macroscopic levels. The reversible enolization redox process, diffusion path, and structure change of molecular crystals have been clearly clarified. Consequently, the materials yield a premier rate capability (70.2 mAh g−1 at 5 A g−1), and excellent cycling stability (retention of 80.3% over 1000 cycles at 2 A g−1). This study extends the boundary of molecular crystal systems for battery chemistry to construct high-performance multivalent ion batteries.