Cocrystals represent an effective approach to manipulate the physicochemical properties of materials at the molecular level. However, understanding the relationship between their complex crystal structures and macroscopic properties has been a challenge. In this paper, based on the advantage of terahertz (THz) spectroscopy in characterizing non-covalent interactions within crystals, we conduct the THz vibrational spectroscopy study on the CL-20/MTNP cocrystal. Firstly, the THz spectra of CL-20, MTNP, and the CL-20/MTNP cocrystal were measured at room temperature. Both absorption positions and intensities of the cocrystal differ from those of its 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 were matched with the calculated vibrations. Furthermore, a vibrational decomposition method was employed to dissect the molecular vibrations into intermolecular and intramolecular vibrations. The vibrational variations of the cocrystal compared to its original components were analyzed. The results reveal that in the cocrystal, the intermolecular vibrational modes of both CL-20 and MTNP molecules undergo alterations compared to their raw materials. This suggests that the non-covalent interactions within the cocrystal modify the original intermolecular interactions between these molecules. Consequently, this enhancement promotes heat transfer between MTNP and CL-20 molecules, thereby improving the thermal stability of the cocrystal. In conclusion, the findings of this study demonstrate that THz vibrational spectroscopy technology is instrumental in establishing a relationship between the molecular structure of cocrystals and their macroscopic properties. This research contributes to advancing our understanding of cocrystal systems and opens up new avenues for material design and optimization.