Polyphenols are a group of secondary plant metabolites widely present in diets and have antagonistic effects on some chronic metabolic diseases, like type 2 diabetes (T2D) and obesity. We attempt to investigate the effects of polyphenols in fruits and vegetables on reducing the risk of T2D and obesity by collecting epidemiological evidence, including cross-sectional survey (CSS), prospective cohort study (PCS), and randomized controlled trial (RCT). Further, we provide possible mechanisms for the anti-diabetic effects including protecting pancreatic β-cells, affecting glucose digestion, absorption, and uptake, and activating glucose/lipid metabolism pathways, while improving obesity by reducing lipid accumulation, regulating intestinal microflora, alleviating inflammation, and reducing food intake. Polyphenols also play an important role in the relationship between T2D and obesity. On the one hand, obesity is a low-grade chronic inflammation causing insulin resistance, so polyphenols can reduce T2D risk by improving obesity. On the other hand, obesity decreases the polyphenols bioavailability by disturbing gastrointestinal microflora, thus increasing T2D risk. These are instructive for diets and bring considerable development value. Therefore, we discussed the hotspots of polyphenols exploitation in the food industry, including masking bitter and astringent taste, ensuring stability, and improving the bioavailability, which provides ideas for polyphenols application in anti-diabetics and anti-obesity.