A new eudesmane-type sesquiterpene, chlorahupetolide R (1), and thirteen known compounds (2–14) were isolated from the roots of Chloranthus henryi Hemsl. var. hupehensis (Pamp.) K.F.Wu. Linderolide E (9) was first reported from the family Chloranthaceae. Atractylenolide III (2), shizukanolide E (3), chloramultilide D (4), shizukanolide F (5), linderolide G (6), 9α-hydroxy-curcolonol (7), linderolide F (8), sarcaglaboside C (10), sarcaglaboside A (11), isofraxidin (12), trans-ferulic acid (13), and ethyl trans-caffeat (14) were first isolated from the investigated plant. In the current research, the structural identification of these compounds was achieved through the analysis of their spectroscopic and spectrometric characteristics. Furthermore, the chemotaxonomic significance of the isolated compounds is discussed briefly.