Calcium ion batteries (CIBs) are pursued as potentially low‐cost and safe alternatives to current Li‐ion batteries due to the high abundance of calcium element. However, the large and divalent nature of Ca2+ leads to strong interaction with intercalation hosts, sluggish ion diffusion kinetics and low power output. Herein, a small molecular organic anode is reported, tetracarboxylic diimide (PTCDI), involving carbonyl enolization (CO↔CO−) in aqueous electrolytes, which bypasses the diffusion difficulties in intercalation‐type electrodes and avoid capacity sacrifice for polymer organic electrodes, thus manifesting rapid and high Ca storage capacities. In an aqueous Ca‐ion cell, the PTCDI presents a reversible capacity of 112 mAh g−1, a high‐capacity retention of 80% after 1000 cycles and a high‐power capability at 5 A g−1, which rival the state‐of‐the‐art anode materials in CIBs. Experiments and simulations reveal that Ca ions are diffusing along the a axis tunnel to enolize carbonyl groups without being entrapped in the aromatic carbon layers. The feasibility of PTCDI anodes in practical CIBs is demonstrated by coupling with cost‐effective Prussian blue analogous cathodes and CaCl2 aqueous electrolyte. The appreciable Ca storage performance of small molecular crystals will spur the development of green organic CIBs. PTCDI is first employed as the anode for aqueous calcium‐ion batteries. The guest‐host chemical bonding and structure evolution of molecular crystals are clearly clarified by simulation and in(ex)‐situ spectroscopy characterizations. This study extends the boundary of molecular crystal systems for electrochemistry to construct high‐performance aqueous multivalent ion batteries.