Herba Siegesbeckiae (HS), derived from the aerial parts of three plants, Siegesbeckia orientalis (SO), S. glabrescens (SG), and S. pubescens (SP), has been used for the treatment of inflammatory diseases in China for centuries. In the present study, hydrodistillation was applied to extract essential oils from dried SO, SG, and SP aerial parts, and chemical composition analysis by gas chromatography–mass spectrometry (GC-MS) led to the identification of a total of 148 compounds (56 in SO, 62 in SG, and 59 in SP). The main components in the essential oils of SO, SG, and SP differed significantly. In vitro anti-inflammatory activity assays showed that SP essential oils (IC50, 0.97 μg/mL) significantly reduced the ability of lipopolysaccharide (LPS)-stimulated RAW264.7 macrophages to release NO, and the SO essential oil (IC50, 14.99 μg/mL) was better than the others at inhibiting the LPS-induced release of cytokine IL-6. Furthermore, the essential oils exhibited antitumor activities (IC50, 37.72–123.16 μg/mL) against Hep3B (liver) and Hela (cervical) cells. Linear regression analysis showed that, caryophyllene oxide peak area percentages showed remarkably high negative correlation coefficients with IC50 values of Hep3B and Hela cytotoxicity, which suggested the contribution of this compound on the cancer cell cytotoxicity of three essential oils. Finally, the ITS1-5.8S-ITS2 region was amplified and sequenced in order to generate genomic reference sequences for each plant. These can be used to identify the origins of the plants, and will assist other research studies related to these three plants.