As one of the most common metabolic diseases, type 2 diabetes (T2D) has become a public health concern with rising global prevalence. Corni fructus (CF), a traditional Chinese herb utilized for centuries as homologous medicinal and food resources, has been widely used to treat glucose and lipid metabolism disorders. However, as a core active ingredient of CF, whether and how morroniside (MOR) improves T2D is still unclear. This study aimed to explore the pathways by which MOR ameliorates T2D in mice induced by high-fat diet (HFD) and low-dose streptozotocin through 16S rRNA gene sequencing. We found that MOR treatment significantly ameliorated body weight loss, hyperglycemia, hyperlipidemia and insulin resistance in T2D mice. In addition, MOR remarkably improved inflammation- and oxidative stress-driven hepatic and pancreatic injuries in the model mice. Mechanistically, MOR rehabilitated the dysregulated diversity and constitution of the gut microbiota in T2D mice, with significant changes in relative abundance in genus such as Lactobacillus, Lachnospiraceae_NK4A136_group, and Lachnospiraceae_UCG-006 which are believed to be highly correlated with serum parameters and insulin resistance in mice with T2D. Therefore, we infer that MOR improves T2D at least partially by maintaining the host microbiota homeostasis, and MOR may be a promising candidate for T2D treatment.