Most DNA methylation occurs in the cytosine of nucleosides. In this study, the absorption coefficients of cytosine and 5-methylcytosine were measured at 0.1-2.0 THz through terahertz time domain spectroscopy (THz-TDS) without being labeled. Our results showed that these important biomolecules had distinct spectral characteristics within this terahertz band. Moreover, structural optimization and lattice dynamics calculations were performed to determine the lattice vibrational motions of both cytosine crystals and 5-methylcytosine crystals using the density functional theory (DFT) and the properly modeled intermolecular potentials. Typically, the lattice vibrational motion simulated the absorption spectrum which indicated that the terahertz technique was able to detect the absorption spectral features of cytosine and 5-methylcytosine. Hopefully, this study provided the molecular background to detect DNA methylation and lay certain foundation for subsequent cancer detection.