As a severe metabolic disease, type 2 diabetes mellitus (T2DM) has aroused increasing public attentions. Resistant starch 3 (RS3), as a starch resistant to enzymatic hydrolysis owing to its special structure, has a good effect on improving insulin resistance and reducing blood sugar in T2DM patients. However, the possible mechanisms were barely interpreted yet. In our research, we aimed to evaluate the effects and the possible mechanisms of RS3 on the treatment of T2DM. ICR mice treated with high-fat diet (HFD) for eight weeks, and then injected with streptozotocin (STZ) (100 mg/kg) to establish the T2DM. We choose the mice with the fast blood glucose (FBG) more than 11 mmol/L as T2DM. After treated for 11 weeks the relevant data was analyzed. According to the results, the FBG was dramatically reduced (p < 0.05), which also downregulated triglyceride (p < 0.01) and total cholesterol (p < 0.01). Additionally, the insulin resistance indexes were significantly reduced (p < 0.01), the homeostasis model assessment-β and insulin-sensitive index were significantly improved (p < 0.01) in RS3 group. Meanwhile, the metabolic profiles of urine were analyzed and 29 potential biomarkers were screened out, including amino acids and lipids. In conclusion, we speculated that the tricarboxylic acid cycle, amino acid metabolism and lipid metabolism played roles in the therapeutic mechanisms of RS3 on T2DM.