The terahertz (THz) absorption spectra of 4- and 5-hydroxysalicylic acid were measured by terahertz time-domain spectroscopy (THz-TDS) in the range of 0.4-2.8 THz. The unit cells of both were calculated by density functional theory (DFT), and the theoretical simulation and experimental data were basically in agreement. To further interpret the origin of the characteristic absorption peaks, vibration characteristics and interactions of the unit cell model were analyzed by using potential energy distribution (PED) and interaction region indicator (IRI) method. The analysis indicated that the absorption peaks of 4- and 5-hydroxysalicylic acid were mainly derived from the vibration mode of dihedral angle torsion, and were closely related to the hydrogen bonds. And the intermolecular weak interaction of both were mainly dominated in quantity by van der Waals interaction. The results show that this is an effective solution to identify isomers and explain the formation mechanism of characteristic absorption peaks by using THz-TDS and combining PED and IRI methods.