In this study, we introduce a terahertz (THz) transmission time-domain polarization detection system, along with a calibration method, capable of effectively identifying the optical characteristics of amino acid enantiomers. Although D- and L-valine enantiomers share highly similar physical properties, they exhibit distinct biological activities. The unique spectral properties of THz radiation enable the efficient detection of biomolecular rotational and vibrational modes. By combining THz time-domain spectroscopy with polarizers and a THz broadband phase shifter, we implement THz time-domain spectroscopic ellipsometry (THz-TDSE). This technique allows for the simultaneous measurement of both phase and amplitude of the electric field, facilitating precise polarization control and extraction of relevant ellipsometric parameters. Our findings indicate that the absorption spectra of D- and L-valine are similar in the THz frequency range. However, when modulating the angle of the polarizer and waveplate, a marked difference in absorption coefficients is observed in the high-frequency region. Specifically, at a polarizer angle of -45°, D-valine exhibits a significantly higher absorption coefficient than L-valine, indicating a stronger absorption capability for electromagnetic waves. This research elucidates the spectral response mechanisms of chiral molecules under specific polarization states and demonstrates the potential of THz spectroscopic ellipsometry for chiral substance identification. It paves the way for new applications of THz optical technologies in biochemistry and materials science.