Terahertz time-domain spectroscopy (THz-TDS) is a new technique in studying the conformational state of a molecule in recent years. In this work, we reported the first use of THz-TDS to examine the denaturation of two photosynthesis membrane proteins: CP43 and CP47. THz-TDS was proven to be useful in discriminating the different conformational states of given proteins with similar structure and in monitoring the denaturation process of proteins. Upon treatment with guanidine hydrochloride (GuHCI),a 1.8 THz peak appeared for CP47 and free chlorophyll a (Chi a). This peak was deemed to originate from the interaction between Chli a and GuHCI molecules. The Chl a molecules in CP47 interacted with GuHCI more easily than those in CP43.