One of the benefits of using terahertz (THz) spectra in characterizing weak interactions is that their anharmonicity can help us to understand the macroscopic properties of crystals. In this study, 2,6-diamino-3,5-dinitropyrazine (ANPZ) was adopted to analyze the anharmonic mechanism of terahertz spectra. First, the temperature-induced anharmonicity was obtained from the THz spectral measurement under heating. Next, density functional theory was used to identify the vibration properties of each absorption. Vibration mode decomposition was then employed to deeply analyze the origins of these anharmonic differences. The results show that the softening of the special intermolecular hydrogen bonding is responsible for the strong anharmonicity. Furthermore, the displacement properties of the atomic temperature factor calculated based on phonon and quasi-simple harmonic approximations also verify the above conclusion. The present study demonstrates that THz spectroscopy can provide insight into the response of hydrogen bonding under heating and can be used as a scientific analysis method for understanding the macroscopic properties of crystals.