Abstract: Biomolecules with different chirality have different or even opposite biological and pharmacological activities. Since vibration and rotation energy levels of many biomolecules lie within the terahertz range, terahertz spectroscopy has emerged as a useful tool for biomolecular identification. Nevertheless, linearly polarized light sources are used in terahertz time-domain spectroscopy, which is ineffective for identifying chiral compounds. We theoretically constructed a circularly polarized Jones matrix using a linearly polarized Jones matrix model. We also calculated the transmission circular dichroism spectrum of the sample based on the difference in transmittance of circularly polarized light, offering a useful technique for describing various chiral compounds. The spectra of (R)-(-)-Ibuprofen and (S)-(+)-Ibuprofen were investigated using a transmission terahertz time-domain spectroscopy system, and the linear polarization biased transmittance and circular polarization transmittance of (R)-(-)-Ibuprofen and (S)-(+)-Ibuprofen were computed. Additionally, the transmittance circular dichroic spectra were calculated, and the two chiral compounds' circular dichroic values reached 0.015, successfully achieving the (R)-(-)-Ibuprofen and (S)-(+)-Ibuprofen recognition effect. This technique serves as a guide for chiral molecule identification and detection using terahertz spectroscopy technology.