Germ rice is a moderately processed products with high germ retention rate (>80%). Electric rice‐cooker and microwave cooking as the most common cooking methods have different effects on starch microstructures, digestibility, rheological behavior, texture, and flavor of germ rice. Microwave‐cooked germ rice contains more short‐range ordered structures and higher crystallinity than electric rice‐cooker cooked germ rice. The starch digestibility of germ rice (i.e., rapidly digestible starch) cooked by microwave under different power and time (50.74%–52.47%) is lower than that of electric rice‐cooker cooked by two modes (60.52%–60.82%). The rheology (modulus and shear viscosity) of germ rice treated by electric rice‐cooker is higher than that treated by microwave. Microwave‐cooked germ rice has lower adhesiveness (164–212 g s) than that cooked in electric rice‐cooker (286–295 g s). Aldehydes are the most abundant volatile components, and play a very important role in germ rice flavor. Microwave cooking can reduce the digestibility of starch and improve the flavor of cooked germ rice. Microwave is expected to be a promising cooking technique for germ rice cooking.