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 which are commonly used in terahertz time-domain spectroscopy are ineffective for identifying chiral compounds. We theoretically construct a circularly polarized Jones matrix by using a linearly polarized Jones matrix model and 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 measured using a terahertz time-domain spectroscopy system, and the linear polarization biased transmittance and circular polarization based transmittance of (R)-(−)-Ibuprofen and (S)-(+)-Ibuprofen were calculated. Additionally, the transmittance circular dichroic spectra of two Ibuprofen were calculated, and the chiral compounds’ circular dichroic values reached 0.015, successfully attaining the (R)-(−)-Ibuprofen and (S)-(+)-Ibuprofen recognition effect. This technique serves as a guide for chiral molecule identification and detection using terahertz spectroscopy technology.