H/D isotopic substitution has been long used to control the physical properties of solid-state materials. However, it is usually futile in weak H-bonded compounds. Herein, we describe large deuteration effects on a weak H-bonded molecular ferroelectric, [CoII(en)3]SO4 (en = ethylenediamine), by anisotropically deuterating the uniaxially aligned complex cations. Upon deuterating the C–H atoms, the ferroelectric temperature window enlarges from 22 to 56 K, and the spontaneous polarization is quadrupled. In contrast, an unprecedented ferroelectric isotopic polymorphism where the ferroelectricity is completely extinguished is observed when the N–H atoms are deuterated. These substantial variations are different from the small shift of a fully deuterated crystal. Detailed crystal structural analyses and theoretical calculations reveal that such surprising behaviors can be ascribed to minute but anisotropic changes in the unit cell (<0.3%) induced by selective deuterations. The anisotropic deuteration could be a promising method to sensitively control the properties and functions of materials.