Terahertz (THz, 1=1012 Hz) wave refers to the frequency in the 0.1~10 THz spectra of electromagnetic radiation. THz time domain spectroscopy (THz-TDS) can provide the structure information of the material and configuration to distinguish different amino acid isomers, and amino acid isomers detection is useful for the quality control of the food and pharmaceutical potency. Leucine and isoleucine are homologous isomers. They have very similar molecular structures, but different chemical and physical properties. Biological macromolecular terahertz absorption is related with intermolecular hydrogen bond vibration and rotational level about the dipole transition, and it can be used for fingerprint identification of molecular dipole transition. In this paper, the terahertz time-domain spectroscopy (THz-TDS) and Fourier transform infrared spectroscopy (FTIR) were used to measure the absorption spectroscopy of leucine and isoleucine at room temperature. A number of different well-resolved THz absorption peaks for the two components were observed, but their infrared absorption peaks were almost overlapped. In parallel with the experiment, the computed vibrational spectra was also obtained by using first principles calculations based on the density functional theory (DFT). The theoretical results fit well with the experimental results.