Owing to various advantages over conventional drying systems, microwave drying technology has been widely applied to vast industrial applications. During microwave drying especially in high moisture content products such as fruits and vegetables, temperature will increase dramatically since they are very responsive to microwave absorption. The characteristics of materials may change with the uncontrolled temperature and result in thermal burning and non-uniform temperature distribution in treated materials. To ensure the effective control without the material degradation, in this paper we propose the automatic phase-controlled of magnetron driver based on temperature detection. The low cost and non-contact infrared temperature measurement is implemented and evaluated in microwave environment. The objective of this proposed control is to automatically control the power output of the magnetron according to the actual product temperature. The hardware component selections and software flowchart are described. The feedback control algorithm based on microcontroller Arduino Mega 2560 is also presented in details. Experimental results of the proposed automatic temperature control of microwave drying system are investigated and verified the effectiveness of the proposed control system.