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Background: During the microwave heating process, the dielectric property of the heated media changes with temperature and time, and the change of temperature at its Low-Temperature (LT) stage and High-Temperature (HT) stage shows different characteristics obviously. Sometimes, hotspots and thermal runaway occur. Methods: Regular control methods are difficult to effectively control the temperature during the whole microwave heating and drying process. To solve this problem, a microwave source power control method based on piecewise fussy PID is proposed. This method uses the k-means clustering to divide temperature change of the heated material into LT stage and HT stage, and adopts fuzzy PID control strategies of different levels and rules based on different temperature change characteristics. Results: This paper studied the fuzzy controller design for the LT and HT stages, respectively and illustrates the engineering way to realize this control method. The simulation result shows that the piecewise fuzzy PID controller reduces the temperature overshoot of the microwave heating process to 1/4 of a regular PID controller and shortens the time for the temperature to reach the target value to 1/3 of the original time. This method also shows good robustness. Conclusion: Therefore, this method, when applied to active control of microwave power, can effectively avoid thermal runaway prone in the heating process and improve the safety and reliability of the microwave heating system.