Microwave digestion is a preferred pretreatment method for agricultural samples because of its quick chemical reaction and minimum loss of analytes. In this research, a feedback temperature controller was developed to control the temperature inside a vessel for the microwave-assisted digestion system. An existing industrial microwave oven was fitted with the temperature controller for controlling inside temperature of the vessel. Four control methods, On/Off, proportional (P), proportional integral (PI), and proportional integral derivative (PID) were used and compared. Experimental results showed that PID control produced best temperature control performance. The PID controller could maintain the temperature of water sample and rice sample in the digestion system with error range of $-2.5{sim}3.3^{circ}C$ and $-1.9{sim}0.5^{circ}C$ at set temperature of $170^{circ}C$, respectively.