The nutritional function of vegetable oil is influenced by different oil extraction methods. In this study, the effects of different processing techniques on the quality of rapeseed oil and animal lipid metabolism were evaluated. Results showed that rapeseed oil obtained by the aqueous enzymatic extraction (AEE) method had the highest polyphenol (152.08 ± 11.44 mg GAE per kg), α-tocopherol (208.97 ± 15.84 mg kg-1), and β-carotene (5.40 mg kg-1) contents and a better oxidation resistance. It was noted in an experiment on rats fed with diets containing rapeseed oils that AEE rapeseed oil reduces total cholesterol (TC), triacylglycerol (TG), low-density lipoprotein cholesterol (LDL-C), aspartate transaminase (ALT) and alanine transaminase (AST) in high-fat diet rats by 27.09%, 11.81%, 35.52%, 31.02% and 27.61%, respectively, and the body and liver weights of rats were decreased. mRNA expression indicated that AEE could significantly down-regulate fatty acid synthase (FAS) and up-regulate acyl-CoA oxidase 1 (ACOX1) gene expression levels (P < 0.05). These results suggested that the AEE method can increase the content of trace active substances in rapeseed oil and ameliorate chronic diseases induced by a high-fat diet.