Pegaeophyton scapiflorum (DHJ) and Solms-laubachia eurycarpa (KGCF) are perennial herbs from the cruciferous family. Historically, these two herbs have been documented to be effective in clearing lung heat and have been widely used clinically to treat symptoms such as pneumonia, colds, and fever. However, due to the scarcity of resources and the similarity of morphological features, the two are often confused in practical applications. In this study, ultra-performance liquid chromatography coupled with quadrupole-Orbitrap high-resolution mass spectrometry (UPLC-Q-Orbitrap HRMS) was employed to comprehensively identify the chemical components of DHJ and KGCF. Leveraging non-targeted metabolomics analysis, we systematically elucidated the compositional disparities between these two herbals and further evaluated their respective biological activities. The UPLC-Q-Orbitrap HRMS technique enabled the identification of 82 compounds. The differences in the chemical compositions of the two herbs could clearly be observed through the chromatographic base peaks and ion flow diagrams. Further screening revealed a total of 41 differential metabolites, including hispidulin, α-linolenic acid, and chlorogenic acid. Additionally, the aqueous extracts of both herbs exhibited good anti-inflammatory and antioxidant activities. Under high-concentration conditions, both extracts significantly alleviated lipopolysaccharide (LPS)-induced cellular inflammatory responses. Moreover, IC50 analysis quantitatively demonstrated that DHJ outperformed KGCF in terms of anti-inflammatory and antioxidant efficacy. However, these results have not yet been validated in vivo. In summary, the present study not only provides a scientific basis for the in-depth analysis of the compositional differences between the two herbs and their anti-inflammatory and antioxidant properties, but also lays a theoretical foundation for the establishment of their quality evaluation system.