The structural transition from hydroquinone clathrates to crystalline alpha-form hydroquinone was observed up to the range of 3 THz frequency as a function of temperatures. We found that all three hydroquinone clathrates, CO2-, CH4-, and CO2/CH4-loaded hydroquinone clathrates, transform into the alpha-form hydroquinone at around 102 +/- 7 degrees C. The resonance peak of the CO2-loaded hydroquinone clathrate at 2.15 THz decreases with increasing temperature, indicating that CO2 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 alpha-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 alpha-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.