Anti-obesity effect of chito-oligosaccharides (CO), resistant starch (RS) and their complexes (CO-RS) was investigated using high-fat fed rats. All of three intervention groups showed anti-obesity effect in the following order: CO-RS > CO > RS. This study revealed CO-RS administration achieved the lightest body weight, the lowest liver weight/index and the highest level of total antioxidant capacity in serum. The RNA sequencing data indicated that peroxisome proliferator-activated receptor (PPAR) pathway was significantly enriched by CO-RS administration. Among the genes involved in PPAR pathway, changes in the expression of Cyp7a1 gene were noticed, indicating an accelerated conversion of cholesterol into bile acids. Furthermore, the current study also revealed that, compared to the high-fat diet control, intervention with CO-RS led to significant reduction in mRNA expression of insulin-induced genes (Insig-1), which did not occur in other two interventions, suggesting a different regulatory pathway affecting lipids metabolism compared with either CO or RS.