Polygonum multiflorum is widely used in the prevention and treatment of hyperlipidemia in traditional Chinese Medicine. In this study, the effects and relevant mechanisms of lipid-regulation by raw Polygonum multiflorum (RPM) were investigated. The results indicated that the basal plasma lipids, such as low-density lipoprotein cholesterol (LDL-C), total cholesterol (TC), and triglycerides (TG), were significantly decreased in RPM treatment groups compared with the model group, especially in the RPM high dose group. The key enzymes involved in lipid metabolism, 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR), fatty acid synthase (FAS) and acetyl-CoA carboxylase (ACC) in plasma were generally reduced after oral administration, which was consistent with the transcription levels of their target genes. In addition, the hepatotoxicity of RPM was investigated, and RPM showed slightly less liver injury than that induced by simvastatin. Histological analysis indicated that the fat vacuoles and steatosis in hepatocytes were relieved after oral administration of RPM extract at a high dose of 16.2 g/kg, which was more obvious than that induced by simvastatin. These results revealed that RPM exerted its lipid-lowering effect by regulating the expression of related genes, and performed better than simvastatin in the treatment of hyperlipidemia.