Far-infrared absorption spectra and refractive indices of hypoxanthine and inosine have been measured by terahertz time-domain spectroscopy (THz-TDS) in the frequency range of 03—16THz at room temperature. The experimental results show that there is a distinct difference between the THz absorption spectra of hypoxanthine and inosine,which suggests that THz-TDS is highly sensitive to molecular structures and the components. Hartree-Fork calculation was used to optimize and simulate the THz spectra obtained by measurement. The low frequency vibrational mode at 14THz of inosine is attributed to the swing and torsion between purine and pentose rings according to the theoretical calculation. There is a linear relationship between the absorption intensity and the concentration of sample,which is consistent with Lambert-Beer's Law. Quantitative analysis of the components of mixtures of hypoxanthine and inosine was carried out by linear regression with non-negative constraint and the relative error was less than 7%. The sources of error were also discussed.