Donepezil hydrochloride is a widely used medication for treating Alzheimer’s disease. This study utilized terahertz time-domain spectroscopy to analyze the fingerprint spectra of donepezil hydrochloride, identifying five characteristic absorption peaks at 1.65, 2.44, 2.56, 3.31, and 3.75 THz. The vibrational spectrum of the donepezil hydrochloride crystal was further examined using solid-state density functional theory. Based on simulation calculations, the characteristic peaks were identified and analyzed in detail, focusing on long-range ordering and weak interaction networks. The results demonstrate that terahertz spectroscopy is an effective tool for studying intermolecular interactions in drug crystals.