Changes in the crystal system of an ionic nanocrystal during a cation exchange reaction are unusual yet remain to be systematically investigated. In this study, chemical synthesis and computational modeling demonstrated that the height of hexagonal-prism roxbyite (Cu_1.8S) nanocrystals with a distorted hexagonal close-packed sulfide anion (S²⁻) sublattice determines the final crystal phase of the cation-exchanged products with Co²⁺ [wurtzite cobalt sulfide (CoS) with hexagonal close-packed S^2– and/or cobalt pentlandite (Co₉S₈) with cubic close-packed S^2–]. Thermodynamic instability of exposed planes drives reconstruction of anion frameworks under mild reaction conditions. Other incoming cations (Mn²⁺, Zn²⁺, and Ni²⁺) modulate crystal structure transformation during cation exchange reactions by various means, such as volume, thermodynamic stability, and coordination environment.