Type 2 diabetes is one of the most common and prevalent metabolic disorders with an ever-increasing rate globally. Metabolic syndromes are characterized by low-grade inflammation and insulin resistance, and are usually accompanied with alteration in the gut microbiota profile. Evidence in recent decades shows that the gut microbiota plays a significant role in the development of metabolic syndromes, and obese individuals have abnormal gut microbiota in composition, abundance and metabolic functions compared to lean individuals. Saskatoon berry is a type of fruit-bearing shrub native in North America. Previous studies found that Saskatoon berry powder (SBp) is capable of reducing inflammation in leptin receptor-knockout (db/db) diabetic mice. Among the anthocyanins in SBp, cyanidin-3-glucoside (C3G) has 3 times higher anti-inflammatory capacity compared to cyanidin-3-galactoside (C3Ga) according to endothelial cell studies. However, research on the effects of Saskatoon berries or contained active components on diabetes and gut microbiota still remains limited. In the present study, the effects of SBp and C3G on diabetes-related physiological indicators and gut microbiota were explored. The result shows that both SBp and C3G significantly decreased elevated levels of glucose, cholesterol, triglyceride, insulin, insulin resistance and inflammatory markers caused by high fat-high sucrose (HFHS) diet. Certain bacteria in the mouse gut, such as Muribaculaceae, was significantly increased by 5% SBp (w/w) or equivalent amount of C3G in 5% SBp. Correlation results revealed that some bacterial families, such as Muribaculaceae and Akkermansiaceae, are negatively associated with hyperglycemia, hypercholesteremia, hyperlipidemia, insulin resistance and low-grade inflammation. Dose-response study found that addition of 1-2.5% (w/w) SBp into HFHS diet already showed an anti-diabetic and anti-inflammatory effects. These findings suggest that Saskatoon berries or related products may have the potential to be applied as a functional food for the prevention or treatment of type 2 diabetes.