Schisandra chinensis (Turcz.) Baill. (S. chinensis) and Schisandra sphenanthera Rehd. et Wils (S. sphenanthera) are called “Wuweizi” in traditional Chinese medicine, and they have distinct clinical applications. To systematically compare the differential characteristics of S. chinensis and S. sphenanthera, this study employed ultra-performance liquid chromatography–quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS) and gas chromatography–mass spectrometry (GC-MS) to construct chemical profiles of these two species from different regions. In total, 31 non-volatiles and 37 volatiles were identified in S. chinensis, whereas 40 non-volatiles and 34 volatiles were detected in S. sphenanthera. A multivariate statistical analysis showed that the non-volatiles tigloygomisin P, schisandrol A, schisantherin C, and 6-O-benzoylgomisin O and the volatiles ylangene, γ-muurolene, and β-pinene distinguish these species. Additionally, the metabolism of oxygen free radicals can contribute to the development of various diseases, including cardiovascular and neurodegenerative diseases. Therefore, antioxidant activities were evaluated using 1,1-diphenyl-2-picrylhydrazyl (DPPH) and 2,2′-azino-bis-3-ethylbenzthiazoline-6-sulphonic acid (ABTS) scavenging assays. The results showed that S. sphenanthera exhibited significantly higher antioxidant potential. A gray relational analysis indicated that the key contributors to the antioxidant activity of S. chinensis were schisandrol A, gomisin G, schisantherin C, pregomisin, gomisin J, and schisantherin B. For S. sphenanthera, the key contributors included gomisin K2, schisantherin B, gomisin J, pregomisin, schisantherin C, schisandrin, gomisin G, schisantherin A, schisanhenol, and α-pinene. The identification of the differential chemical markers and the evaluation of the antioxidant activities provide a foundation for further research into the therapeutic applications of these species. This innovative study provides a robust framework for the quality control and therapeutic application of S. chinensis and S. sphenanthera, offering new insights into their medicinal potential.