The effects of different thermal processing methods on the bioactivity of germinated highland barley (GHB), and the regulatory effects of microwave-treated GHB on glucose and lipid metabolism in mice fed a high-fat diet (HFD) were investigated in this study. GHB was first processed by microwaving, baking, stir-frying, and steaming, followed by the determination of its antioxidant properties and in vitro starch digestion characteristics. Additionally, a HFD-induced obese mouse model was established to study the regulatory effects of microwave-treated GHB on glucose and lipid metabolism and gut microbiota. Except for steaming, the other thermal processing methods significantly enhanced the antioxidant capacity of GHB. The scavenging rates for •OH, DPPH, and ABTS+ free radicals of the microwave-treated group reached 49.35%, 73.56%, and 89.15%, respectively. Thermal processing generally increased the starch hydrolysis rate, but the microwave-treated group exhibited the lowest starch hydrolysis rate (65.03%) and predicted glycemic index (62.97). Moreover, microwave-treated GHB significantly inhibited body weight gain, reduced blood glucose levels, improved lipid profiles and liver function, and enhanced the antioxidant capacity of the liver in HFD mice. It also optimized the structure of the gut microbiota, enhanced microbiota diversity, increased the abundance of Bacteroidetes, and elevated the content of short-chain fatty acids. In conclusion, this study demonstrates that thermal processing can enhance the antioxidant and starch digestion abilities of GHB, with microwave treatment granting the additional advantage of regulating the gut microbiota. These findings provide a theoretical basis for the intervention of metabolic disorders using GHB and the development of GHBrelated functional foods.