Cocrystal is constructed to improve physicochemical properties of active pharmaceutical ingredient and prevent polymorphism via intermolecular interactions. However, recent examples on cocrystal polymorphs display significantly different properties. Even though some analytical techniques have been used to characterize the cocrystal polymorphic system, it remains unclear how intermolecular interactions drive and stabilize the structure. In this work, we study the cocrystal polymorphs of nifedipine (NFD) and isonicotinamide (INA) using terahertz (THz) spectroscopy. Form I and form II of NFD-INA cocrystals show spectral fingerprints in THz region. Temperature-dependent THz spectra display distinguished frequency shifts of each fingerprint. Combined with solid-state density functional theory (DFT) calculations, the experimental fingerprints and their distinct responses to temperature are elucidated by specific collective vibrational modes. The vibrations of hydrogen bonding between dihydropyridine ring of NFD and INA are generally distributed below 1.5 THz, which play important roles in stabilizing cocrystal and preventing the oxidation of NFD. The rotations of methyl group in NFD are widely distributed in the range of 1.5–4.0 THz, which helps the steric recognition. The results demonstrate that THz spectroscopy is a sensitive tool to discriminate cocrystal polymorphs. It has the potential to be used as a non-invasive technique for pharmaceutical screening.