The aim of this study is to investigate the main active components of Gegen (Puerariae Lobatae Radix) on atherosclerosis and its mechanism of action. Bioinformatics analysis showed that (3-sitosterol was the most likely active ingredient to mediate the anti-atherosclerotic effects. In vivo experiments showed that (3-sitosterol inhibited plaque formation and platelet activation, and decreased serum total cholesterol (TC) and triglyceride (TG) levels. In vitro experiments showed that (3-sitosterol can inhibit lipid deposition and phenotypic transformation of vascular smooth muscle cells (VSMCs). However, knocking down catalase (CAT), the direct target of (3-sitosterol, not only promoted lipid deposition and phenotypic transformation of VSMCs, but also activated the PI3K/Akt/mTOR pathway, and the mTOR inhibitor (ink-128) can eliminate the effect of CAT knockdown, suggesting that (3-sitosterol may inhibit lipid deposition and phenotypic transformation of VSMCs by activating CAT and silencing the PI3K/Akt/mTOR signaling pathway, thereby alleviating atherosclerosis.