A combination of germination and extrusion was applied to whole grain corn to increase its nutritional composition, functional properties and non-anthocyanin polyphenol profile, especially related to in vitro hypoglycemic effects. Individual germination and extrusion both led to an increase in soluble dietary fiber and lysine, methionine, tryptophan content, while insoluble dietary fiber content decreased. Extruded germinated whole corn flour (EGWCF) had a higher water absorption and solubility index, showing 103 and 575% increases over untreated ones, respectively. Germination increased free, bound phenolic acid and bound flavonoid content to 169, 230 and 311%, respectively. The total phenolic acid and flavonoid content of EGWCF was 260 and 249% of WCF, respectively. Germination increased the polyphenol composition from 12 to 15 species. Phenolic profiles of EGWCF exhibited collective effects, showing three new phenolic compounds. Polyphenol extracts showed more potent activity against alpha-glucosidase rather than alpha-amylase. Free form polyphenols had stronger inhibitory activity than the bound forms. Compared with WCF, free and bound polyphenol extracts from EGWCF increased the anti-alpha-glucosidase activity by 221 and 40%, and increased the anti-alpha-amylase activity by 105 and 108%.