In traditional Korean medicine (TKM), blood stasis syndrome (BSS) is defined as a condition that is stagnant due to poor circulation of blood in the body. Recent studies have revealed that blood stasis is related to metabolic diseases such as obesity, atherosclerosis, and type2 diabetes. The BS11 is a typical prescription for treating blood stasis in TKM, but the few studies reported the effect of BS11 on metabolic diseases. In this study, we administered BS11 (300 mg/kg/day and 600 mg/kg/day) to western diet (WD)‐induced obesity mice. Also, we applied liquid chromatography mass spectrometry (LC/MS)‐based lipidomics, and metabolomics analysis. In our results, WD‐induced obese mice weighted more than normal diet mice, especially at 13 weeks. On the other hand, BS11 groups showed no significant change compared to WD group. In histopathological experiments, it is considered that BS11 has favorable inhibitory effects on the WD‐induced organ damages. In both concentrations of BS11 groups, aortic wall thickening, lipid deposition with MCP‐1 and expressions of ICAM‐1 and VCAM‐1 were reduced. Hepatic steatosis, adipocyte hypertrophy and inflammatory cell infiltration were improved by BS11 treatment. In particular, BS11 reduced cholesterol levels in WB mice, one of the major causes of atherosclerosis. Moreover, we confirmed the unique lipid profile after BS11 treatment. Thus, we investigated the hepatic genes related cholesterol metabolism. BS11 treatment significantly altered liver X receptor alpha (LXRα) regulated cholesterol 7 alpha‐hydroxylase (CYP7A1) and ATP‐binding cassette sub‐family G member 8 (ABCG8), indicating alteration of cholesterol excretion by BS11 treatment. In conclusion, it is expected that appropriate treatment of BS11 will be provided a novel therapeutic candidate for blood stasis syndrome through improve cholesterol metabolism.