Objective To compare changes in intestinal flora and the characteristics of short-chain fatty acid metabolism in hyperlipidemic rats induced by two different high fat diets, and to explore the possible mechanism of hyperlipidemia from the viewpoint of host-intestinal flora metabolism. Methods SPF SD rats were divided into a normal diet group (CG) and two high fat diet groups (HFD1 and HFD2). Rats were fed an 80 g high fat diet and unlimited maintenance diet. After 8 weeks, serum levels of total cholesterol (TC), triglyceride (TG), low density lipoprotein cholesterol (LDL-C), and high density lipoprotein cholesterol (HDL-C) were measured. Pathological changes in liver tissue and perirenal fat were observed by hematoxylin-eosin (HE) staining. Colon contents were collected for 16S rDNA high-throughput sequencing to assess changes in the structure and function of intestinal flora and the intestinal contents of short-chain fatty acids. Results Compared with the CG group, food intake was decreased and body weight was increased, serum TC, TG, and LDL-C were increased significantly, liver tissue showed obvious steatosis and perirenal fat showed inflammatory lesions in HFD1 and HFD2 groups. After high fat intervention, the relative abundance of intestinal microflora in rats was changed significantly and sex differences were observed, in which the relative abundance of Lactobacillus was decreased significantly, and the structure and function of Lactobacillus were decreased significantly, including total shortchain fatty acids, acetic acid, butyric acid, and isobutyric acid. Conclusions The two kinds of high-fat diet caused hyperlipidemia in rats. The pathogenesis was essentially the same and related to lipid metabolism and intestinal flora disorder. Daily restriction of a certain amount of high fat diet reduced the effect of high fat on appetite and improved stability of rat hyperlipidemia model establishment.