A new prenylated naphthoquinoid, named (3R,4aR,10bR)-3,10-dihydroxy-2,2-dimethyl-3,4,4a,10b-tetrahydro-2H-naphtho[1,2-b]-pyran-5H-6-one (1), was isolated from the aerial parts of Clinopodium chinense (Benth.) O. Kuntze, together with six known compounds: apigenin (2), luteolin (3), neoeriocitrin (4), naringenin (5), narirutin (6), and didymin (7). Neoeriocitrin was isolated for the first time from the species C. chinense. Their structures were elucidated by spectroscopic methods, including 1D, 2D (1H-1H-COSY, HSQC, HMBC and NOESY) NMR, HR-ESI-MS. The absolute configuration of 1 was determinated using the CD method. We highlight that the structure of 1 is characterized by a rarely seen prenylated naphthoquinoid framework.