Cocrystals represent an effective method to manipulate the physicochemical properties of materials at a molecular level. However, understanding the relationship between their complex crystal structures and macroscopic properties is a challenge. In this paper, by using terahertz (THz) spectroscopy to characterize non-covalent interactions within crystals, the THz vibrational spectra of the CL-20/MTNP cocrystal are studied. Firstly, the THz spectra of CL-20, MTNP, and the CL-20/MTNP cocrystal are measured at room temperature. Both absorption positions and intensities of the cocrystals differ from those of their original components, confirming the unique advantage of terahertz spectroscopy in cocrystal identification. Secondly, the THz vibrational features of the three materials are calculated based on density functional theory (DFT). Then, the experimental absorptions are matched with the calculated vibrations. Furthermore, a vibrational decomposition method is employed to decompose the molecular vibrations into intermolecular and intramolecular vibrations. The vibrational variations of the cocrystal compared with its original components are analyzed. The results reveal that in the cocrystal, the intermolecular vibrational modes of both CL-20 and MTNP molecules have changed compared with their raw materials. This indicates that the non-covalent interactions in the cocrystal have changed the original intermolecular interactions of these molecules. Consequently, this enhancement promotes the heat transfer between MTNP and CL-20 molecules, thereby improving the thermal stability of the cocrystal. These findings in this study demonstrate that the THz vibrational spectroscopy technology helps establish a relationship between the molecular structure of cocrystal and its macroscopic properties. This research contributes to deepening our understanding of cocrystal systems and opens up a new way for designing and optimizing materials.