Metal–organic frameworks (MOFs) are prone to exhibit phase transitions under stimuli such as changes in pressure, temperature, or gas sorption because of their flexible and responsive structures. Here we report that a dense MOF, ((CH3)2NH2)2[Li2Zr(C2O4)4], exhibits an abrupt increase in proton conductivity from < 10^{–9} to 3.9 × 10^{–5} S/cm at 17 °C (activation energy, 0.64 eV) upon exposure to humidity. The conductivities were determined using single crystals, and the structures were analyzed by X-ray diffraction and X-ray pair distribution function analysis. The initial anhydrous structure transforms to another dense structure via topotactic hydration (H2O / Zr = 0.5), wherein one-fourth of the Li ions are irreversibly rearranged and coordinated by water molecules. This structure further transforms into a third crystalline structure by water uptake (H2O / Zr = 4.0). The abrupt increase in conductivity is reversible and is associated with the latter reversible structure transformation. The H2O molecules coordinated to Li ions, which are formed in the first step of the transformation, are considered to be the proton source, and the absorbed water molecules, which are formed in the second step, are considered to be proton carriers.