Germinated brown rice (GBR) has high nutritional and health-promoting value, but the influence mechanism of microwave vacuum drying (MVD) on the quality properties of GBR is still unclear. This study investigated the effects of MVD parameters including microwave intensities (9, 12, and 15 W/g), drying temperatures (50, 60, and 70 °C), and vacuum pressures (0.03, 0.05, and 0.07 MPa) on the drying characteristics, quality attributes and starch structure of GBR. A falling-rate phase dominated the MVD process of GBR and temperature-controlled MVD significantly preserved the GABA content in GBR. MVD caused microstructural changes with rearrangement and gelatinization of starch granules in GBR. For the GBR under MVD, increasing the drying temperature resulted in a significant decrease in enthalpy (ΔH) and an increase in the degree of starch gelatinization (DSG) (P < 0.05), however, no significant effect of microwave intensity and vacuum pressure on ΔH and DSG (P > 0.05) was found. MVD reduced the relative crystallinity but hardly changed the crystal type or formed functional groups of starch molecules in GBR. Overall, temperature-controlled MVD conduced to the final quality of GBR. This study may provide a potential method to improve the quality attributes of GBR in product development applications.