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 03—16THz 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 14THz 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.