We employed terahertz time-domain spectra (THz-TDS) and Fourier transform infrared spectra (FTIR) to measure the terahertz spectroscopy of L-ascorbic acid and thiamine in the frequency region ranging from 0.10 to 3.50 THz. Molecular models of two vitamins have been shown, and based on above two spectroscopies, we compared the differences about the absorption spectra between the L-ascorbic acid and the thiamine. The measured results show that the absorption spectra obtained based on THz-TDS and FTIR are completely consistent in the frequency range of 0.70 to 3.00 THz. New fingerprint peaks obtained by the FTIR in the low frequency region from 0.30 to 0.50 THz in terms of high sensitive silicon bolometer detector, which are not found by the THz-TDS. Furthermore, several bands at 8.75, 8.85, 9.00, 9.30 and 10.30 THz, fingerprint peaks have been found in the frequency region from 8.00 to 12.00 THz for the thiamine sample obtained by the FTIR. Measurement results indicate the absorption spectra depend on the ratio of polyethylene powder mixed with the L-ascorbic acid. L-ascorbic acid has a lower absorption ability at THz band, so pure samples should be used for testing experiment. In addition, we calculated the refractive index for the two samples. This study has important implications for the discriminatory analysis of vitamins and the establishment of vitamin spectroscopy standard database.