We selected an array of whole grains (WGs), including highland barley, buckwheat, coix seed, foxtail millet, barley, oats, proso millet and sorghum to determine their carbohydrates profile before and after extrusion-expansion, estimated glycemic index (GI) and fermentation characteristics. Our findings reveal that the extrusion processing can significantly influence the structural properties and digestibility of starch. A notable rise in the total dietary fiber (TDF) content was found in foxtail millet, barley and sorghum (p < 0.05) after extrusion. Digestion results of extruded whole grains (EWGs) suggested that coix seeds, oats, and sorghum after extrusion can better manage glycemic index (GI) values due to low starch hydrolysis degree and higher resistant starch (RS) and slowly digestible starch (SDS) content. EWGs with higher TDF content (HE, FE, SE, OE and BE) demonstrated greater SCFA yield, with extruded highland barley exhibiting a superior capacity for generating propionic acid and butyric acid. Extruded barley, buckwheat, oats, and proso millet significantly boosted microbial diversity. All eight EWGs notably curtailed Bilophila growth and fostered beneficial bacteria such as Prevotella, Megamonas, Megasphaera, Bifidobacterium, Parabacteroides and Phascolarctobacterium. This study provides a robust scientific foundation for the application of extrusion technology in functional WGs products.