The structural transition from hydroquinone clathrates to crystalline α-form hydroquinone was observed up to the range of 3 THz frequency as a function of temperatures. We found that all three hydroquinone clathrates, CO(2)-, CH(4)-, and CO(2)/CH(4)-loaded hydroquinone clathrates, transform into the α-form hydroquinone at around 102 ± 7 °C. The resonance peak of the CO(2)-loaded hydroquinone clathrate at 2.15 THz decreases with increasing temperature, indicating that CO(2) guest molecules are readily released from the host framework prior to the structural transformation. This reveals that the hydroquinone clathrates may transform into the stable α-form hydroquinone via the metastable form of guest-free clathrate, which depends on guest molecules enclathrated in the cages of the host frameworks. A strong resonance of the α-form hydroquinone at 1.18 THz gradually shifts to the low frequency with increasing temperature and shifts back to the high frequency with decreasing temperature.