Aim To investigate the anti-atherosclerosis mechanism of phlegm-clearing treatment, Gualou Xiebai Banxia Decocation(GXBD), a typical decoction of phlegm-clearing treatment was studied in the effect of modulating the metablism of proteoglycans in aorta. Methods Thirty rabbits were randomly divided into three groups, normal group, model group, and treatment group. Model group and treatment group were fed with high lipid food to induce the pathological change of atherosclerosis, besides, treatment group was given with GXBD everyday, while normal group was fed with normal food as control. After six weeks, blood fat and aorta atherosclerosis pathological changes was examined, proteoglycans was extracted and turned to glycosaminoglycan by enzymolysis, electrophoretic analysis was used to determine the consist and content of every kinds of glycosaminoglycan. Results The atherosclerosis pathological changes was evident, in conrtol group, the contents of cholesterin and low density lipoprotein were 13.43±3.12 mmol/L and 8.53±1.37 mmol/L, the contents of chondroitin and dermatan sulfate were 21.93±1.82 mg/g, 15.56±1.61 mg/g; whereras in model group, cholesterin and low density lipoprotein increased to 23.63±4.31 mmol/L, 15.63±1.27 mmol/L (P<0.01), chondroitin and dermatan sulfate increased to 31.23±1.41 mg/g, 19.36±1.64 mg/g (P<0.01 or P<0.05); contrast to model group, the atherosclerosis pathological changes in treatment group were evidently imporved, the contents of chondroitin and dermatan sulfate decreased to 22.33±1.58 mg/g, 14.36±1.71 mg/g(P<0.01 or P<0.05), the content of cholesterin, low density lipoprotein of blood shows little changes. Conclusions The gualou xiebai banxia decocation exerts the anti-atherosclerosis effect by modulating the metablism of proteoglycans rather than modulating the blood fat.