The characteristic absorption spectra of three positional isomers of hydroxybenzoic acid are measured using a terahertz time-domain spectroscopy system (THz-TDS) in the 0.6–2.0 THz region at room temperature. Significant differences in their terahertz spectra are discovered, which indicates that THz-TDS is an effective means to identify positional isomers. In order to simulate their spectra, the seven molecular clusters of 2-, 3-, and 4-hydroxybenzoic acid (2-, 3-, and 4-HA) are calculated using the DFT-D3 method. Additionally, the potential energy distribution (PED) method is used to analyze their vibration modes. The analysis indicates that the vibration modes of 2-HA are mainly out-of-plane angle bending and bond angle bend in plane. The vibration modes of 3-HA are mainly bond length stretch and dihedral angle torsion. The vibration modes of 4-HA are mainly bond angle bend in plane and dihedral angle torsion. Interaction region indicator (IRI) analysis is used to visualize the location and type of intermolecular interactions in 2-, 3-, and 4-HA crystals. The results show that the weak interaction type of 2-, 3-, and 4-HA is dominated by van der Waals (vdW) interaction. Therefore, we can confirm that terahertz spectroscopy detection technology can be used as an effective means to identify structural isomers and detect the intermolecular interactions in these crystals. In addition, it can explain the absorption mechanism of terahertz waves interacting with matter.