A systematic phytochemical investigation of the aerial parts of Dracocephalum moldavica led to the isolation of 1 new and 16 known compounds. Based on spectroscopic analyses, the new compound was elucidated as a flavonoid glycoside, acacetin-7-O-(4″-acetyl)-glucopyranoside (1). The 16 known compounds were identified as: 9 flavonoids (2-10), 2 lignans (11-12), 4 triterpeniods (13-16) and 1 menthane-type monoterpenoid (17). All the 17 compounds were reported for the first time from D. moldavica. Compound 1 exhibited mild radical scavenging activity against 2,2-diphenyl-1-picrylhydrazyl (DPPH). Although compound 17, named as citrylidene malonic acid, was a known compound, it possessed an uncommon tricyclic dilactone skeleton, the structure was secured by X-ray crystallography. In addition, compound 17 was tested for cytotoxic activity against A549 cell line, only weak cytotoxicity was shown.