Tunnel microwave heating technology has been widely used in grain drying. Development of a reliable control strategy for this process plays an essential role in improving the overall efficiency and productivity. Thus, a tunnel microwave heating system, which can automatically and continuously adjust microwave power and control sample temperature, is designed and used in rice drying. The rice sample is first dried with three fixed microwave power levels to obtain the prior knowledge of tunnel microwave drying process. An expert control system (ECS) based hierarchical control strategy is then developed to regulate the microwave power and track the desired drying temperature. The effectiveness of the proposed control strategy is validated by experiment carried out in the system, which demonstrates that the proposed strategy can commendably control the rice temperature.