Structure-defined metal–organic frameworks (MOFs) are of interest because rational design and construction allow us to develop good proton conductors or possibly control the proton conductivity in solids. We prepared a highly proton-conductive MOF (NH4)2(adp)­Zn2(ox)3·nH2O (abbreviated to 1· n H 2 O, adp: adipic acid, ox: oxalate, n = 0, 2, 3) having definite crystal structures and showing reversible structural transformations among the anhydrate (1), dihydrate (1·2H 2 O), and trihydrate (1·3H 2 O) phases. The crystal structures of all of these phases were determined by X-ray crystallography. Hydrogen-bonding networks consisting of ammonium ions, water molecules, and carboxylic acid groups of the adipic acids were formed inside the two-dimensional interlayer space in hydrated 1·2H 2 O and 1·3H 2 O. The crystal system of 1 or 1·2H 2 O (P21/c, No. 14) was changed into that of 1·3H 2 O (P1̅, No. 2), depending on water content because of rearrangement of guests and acidic molecules. Water molecules play a key role in proton conduction as conducting media and serve as triggers to change the proton conductivity through reforming hydrogen-bonding networks by water adsorption/desorption processes. Proton conductivity was consecutively controlled in the range from ∼10–12 S cm–1 (1) to ∼10–2 S cm–1 (1·3H 2 O) by the humidity. The relationships among the structures of conducting pathways, adsorption behavior, and proton conductivity were investigated. To the best of our knowledge, this is the first example of the control of a crystalline proton-conducting pathway by guest adsorption/desorption to control proton conductivity using MOFs.