Taking the mixing time and mixing times of double-layer stirred microwave reactor as the correlative characteristic variables, the fuzzy PID control method was adopted to control the material double-layer stirring structure of microwave reactor. Glass and alumina beads were used as the mixing medium to adjust the error feedback of the double-layer stirring. With the adaptive control, the material mixing uniformity control law of the double-layer stirred microwave reactor was established, and the material mixing uniformity was realized by obtaining the optimal control function of material mixing uniformity control. The simulation results showed that the uniformity of material mixing control and the stability of material mixing uniformity control in the double-layer stirred microwave reactor were better.