N,N’‐dihydroxy‐1,4,5,8‐naphthalenetetracarboxdiimide (NDI−(OH)2) has attracted much attention in recent years, because its doubly deprotonated state, (O−NDI−O)2−, has metal‐coordination ability and characteristic electronic transition useful for designing electronic and optical functions. In contrast, a molecular crystal with the mono‐deprotonated (HO−NDI−O)− ion remains unknown. We herein report an organic crystal containing non‐disproportionated (HO−NDI−O)− ions, which are connected by very strong O−H−O hydrogen bonds. Its lowest energy absorption band (450 to 650 nm) is observed in between that of NDI−(OH)2 (380 nm) and isolated (O−NDI−O)2− (500 to 850 nm) species, consistent with the molecular orbital calculations. This absorption originates from the electronic transition from deprotonated imide‐based orbitals to NDI‐core orbitals, which can be influenced by the hydrogen bonds around imide group. Consequently, the optical properties of NDI−(OH)2 can be modulated by the stepwise deprotonation and hydrogen‐bonding interactions.