We investigated molecular structure change of d- and l-glucose by proton beam irradiation of 7.8 MeV, using terahertz time-domain spectroscopy. Both glucose pellets exposed to the irradiation of 1013, 4 × 1013, 6 × 1013, and 8 × 1013 particles/cm2 of the particle’s fluence, were characterized using complex refractive indices in terahertz frequency region. We found that fingerprints of two types of glucose in terahertz frequency were disappeared above 8 × 1013 particles/cm2. Crystallinity breaking and molecular structure change by proton irradiation was reaffirmed using X-ray diffraction (XRD) and Fourier transform infrared (FTIR) spectroscopy.