Rabdosia rubescens, a Chinese herbal medicine with anticancer properties, contains two active ingredients: oridonin and ponicidin. Both compounds exhibit antitumor effects by inducing tumor cell apoptosis and autophagy and inhibiting tumor cell proliferation. To further explore the differences in molecular structure and pharmacological properties between the two substances, this study employs Terahertz Time-Domain Spectroscopy (THz-TDS) to investigate the spectral characteristics of oridonin and ponicidin in the frequency range of 0.1 to 2.3 THz. The crystal structures of the two substances are simulated using Materials Studio software and Density Functional Theory (DFT), yielding their spectra and molecular vibration modes, which elucidate the mechanism underlying the peak generation. The consistency between experimental and simulation results confirms the reliability of the experimental findings. Thus, THz spectroscopy can effectively distinguish between these two substances. Finally, a THz detection is performed on Rabdosia rubescens capsules purchased from the market, revealing the presence of absorption peaks for both substances in their absorption spectra. This provides a new approach for detecting active ingredients in Chinese herbal medicines.