Calcium-deficient zinc-containing calcium phosphate (ZnAP), which has sustained zinc release properties that are effective for treating osteoporosis, can be efficiently synthesized as a biomaterial through wet grinding. To elucidate the physicochemical mechanism of these mechanochemical syntheses, ground products were obtained from the starting material powder (S-CP), consisting of calcium hydrogen phosphate dihydrate (CHPD), calcium oxide (CaO), and zinc oxide (ZnO), by wet and dry grinding for 0–3 h in a centrifugal ball mill. The ground S-CP products were analyzed using powder X-ray diffraction (XRD) and near-infrared spectroscopy (NIRS); the crystal transformations and molecular interactions of the ground products were kinetically analyzed. The XRD and second-derivative NIRS results indicate that the S-CP is primarily transformed into ZnAP via amorphous solid formation in wet grinding, and the reaction follows a consecutive reaction model. In contrast, in dry grinding, the ground product of CHPD and CaO is transformed into an amorphous solid following an equilibrium reaction model; however, ZnO is predominantly not transformed and remains crystalline.