We theoretically investigated a significant contraction of the hydrogen-bonding O center dot center dot center dot O distance upon H/D substitution in our recently developed purely organic crystals, kappa-H-3(Cat-EDT-ST)(2) (H-ST) and its isotopologue kappa-D-3(Cat-EDT-ST)(2) (D-ST), having pi-electron systems coupled with hydrogen-bonding fluctuation. The origin of this geometrical H/D isotope effect was elucidated by using the multicomponent DFT method, which takes the H/D nuclear quantum effect into account. The optimized O center dot center dot center dot O distance in HST was found to be longer than that in D-ST due to the anharmonicity of the potential energy curve along the O-H bond direction, which was in reasonable agreement with the experimental trend. (C) 2017 Elsevier E.V. All rights reserved.