Hyperlipidemia is associated with many diseases and considered the main contributing factor in the development of metabolic syndrome. The traditional Mongolian medicine Dracocephalum moldavica L. (D. moldavica) is commonly consumed as a tea (non-Camellia tea) for the prevention and treatment of coronary heart disease, hypertension, atherosclerosis, and other diseases. Here, we attempted to investigate the hypolipidemic activity and mechanisms underlying the active components of D. moldavica. First, the mechanism underlying the lipid accumulation-reducing effects of the D. moldavica ethanol extract was determined using in vitro experiments, and four polar fractions were screened for activity. Then, the effect of the ethyl acetate fraction of D. moldavica (EAD) on lowering blood lipid was confirmed in vivo. The combination of network pharmacological and serum pharmacochemistry analyses showed that apigenin, luteolin, and naringenin of EAD existed in prototype form in the drug-containing serum of rats. We also determined the content of the three active ingredients in EAD. Finally, in vitro experiments showed that apigenin, luteolin, and naringenin improved oleic acid-induced lipid accumulation in HepG2 cells by regulating the PPAR signaling pathway (PPARα, CPT1, and FABP3). Our findings provide mechanistic insights and application prospects for the prevention and treatment of hypolipidemia using D. moldavica.