The present study was designed to investigate the therapeutic effcts of Moutan Cortex (CM, root bark of Paeonia suffruticosa Andr) and Paeoniae Radix Rubra (PR, root of Paeonia veitchii Lynch) on metabolic disorders, focusing on the infuence of CM and PR on the obesity-related gut microbiota homeostasis. The diet-induced obese (DIO) mouse model was used to test the therapeutic effects of CM and PR. The mice were orally administered with CM and PR for 6 weeks, and oral glucose tolerance test (OGTT) and insulin tolerance test (ITT) were performed to evaluate the insulin sensitivity of the mice. Sterol-regulatory element binding proteins (SREBPs) and their target genes were measured by quantitative RT-PCR. High-throughput 16S ribosomal RNA (16S rRNA) gene sequencing technology was used to determine the composition of gut microbiota, and the metabolites in serum were analyzed by GC-MS. Our results indicated that CM and PR combination alleviated obese and insulin resistance in the DIO mice, leading to increased glucose uptake and gene expression in muscle and liver, and down-regulated SREBPs and their target genes in liver. Interesting, neither the CM-PR extracts, nor the major components of CM and PR did not affect SREBPs activity in cultured cells. Meanwhile, CM and PR significantly modulated the gut microbiota of the high-fat diet (HFD) treated mice, similar to metformin, and CM-PR reversed the overall microbiota composition similar to the normal chow diet (NCD) treated mice. In conclusion, our results provide novel mechanisms of action for the effects of CM and PR in treating DIO-induced dysregulation of sugar and lipid metabolism.