Advanced glycation end products (AGEs) are closely associated with obesity mediated metabolic dysfunction, including hepatic injury, dyslipidemia, and glucose intolerance. Oenothera biennis seed (OBS) has been reported to have antioxidant and anti-inflammatory properties, but the protective effects against AGE-induced metabolic disorder remain unclear. In this study, a CML-high fat diet (HFCML) mouse model was used to evaluate the effects of the OBS extract. OBS supplementation significantly attenuated kidney hypertrophy induced by HFCML diet. The serum alanine aminotransferase and aspartate aminotransferase levels were elevated in the HFCML group, and were reduced significantly by OBS administration. OBS administration also improved lipid metabolism by lowering triglycerides and low-density lipoprotein cholesterol. Furthermore, OBS administration enhanced glucose tolerance. Overall, OBS extract mitigates HFCML-induced metabolic dysfunction by improving liver function, normalizing lipid profiles, and enhancing glucose tolerance, highlighting its potential as a functional food ingredient for the prevention of AGE-associated metabolic diseases such as non-alcoholic fatty liver disease and insulin resistance.