Dietary interventions are receiving increasing attention for maintaining host health and diminishing disease risk. This study endeavored to elucidate the intervention effect of chlorogenic acid coupled with extruded rice starch (CGA-ES) in mitigating lipid metabolism disorders induced by a high-fat diet (HFD) in rats. First, a significant increase in resistant starch (RS) and a decrease in the predicted glycemic index (pGI) were observed in CGA-ES owing to the formation of an ordered structure (Dm, single helix, and V-type crystalline structure) and partly released CGA. Compared to a physical mixture of starch and chlorogenic acid (CGA + S), CGA-ES showed a more potent effect in alleviating lipid metabolism disorders, manifesting as reduced levels of blood glucose, serum total cholesterol (TC), triglycerides (TG), aspartate aminotransferase (AST), alanine transaminase (ALT) and alkaline phosphatase (AKP), as well as body weight. It is correlated with an improvement in the gut microecology, featuring bacteria known for cholesterol reduction and butyrate production (Butyricicoccus, Bifidobacterium, Fusicatenibacter, Turicibacter, and Enterorhabdus), along with bile acid, butyrate and PG (PG (17:0/16:0) and PG (18:1/16:0)). The RS fraction of CGA-ES was found to be the main contributor. These findings would provide evidence for future studies to regulate lipid metabolism disorders, and even obesity using CGA-ES.