In this research, the objective was to optimize the drying process of Astragalus by investigating the effects of microwave vacuum drying parameters, including temperature (30, 35, 40, 45, and 50 °C) and slice thickness (2, 3, 4, 5, and 6 mm). In addition, utilizing COMSOL 6.0 finite element analysis software, we delved into the distribution of heat and moisture during the drying process. The results revealed that drying temperature played a significantly greater role than slice thickness in determining the drying dynamics. The thermal and mass transfer mechanism indicated that the whole drying process conforms to the microwave radiation mechanism and the basic principle of electromagnetic heating. In the case of low temperatures and thinner slice sizes, the more polysaccharide content was retained; The total phenol content peaked when the slice thickness was 5 mm; The increase of slice thickness was not conducive to the retention of total flavonoids content. The potent antioxidant capacity was detected at a temperature of 40 °C, with slice thickness having a negligible effect on this capacity; Low temperatures were beneficial for the preservation of active ingredients. Compared with the scanning electron microscope, the structure appeared more uniform at a temperature of 50 °C. Based on the analysis of the kinetic characteristics of microwave vacuum drying of Astragalus and the quality achieved under various drying conditions, the results of the study can provide valuable guidance for controlling the quality of microwave vacuum drying of Astragalus under different drying requirements.