Conversion efficiency is the primary performance metric of a periodically poled lithium niobate (PPLN) waveguide and strongly correlates with temperature. Multichannel waveguides are limited by process issues; accordingly, ensuring consistency between each waveguide channel is difficult. This paper proposes an automatic temperature control method for multichannel waveguides. In this method, number of photons detected using multiple single photon detectors corresponding to the multichannel waveguide is obtained by field-programmable gate array (FPGA) chips. Thereafter, the photon number data of each channel is processed using equalization algorithms to determine the optimal temperature working point of the multichannel waveguide and achieve automatic adjustment of the waveguide temperature. FPGA chips are used in this study to achieve TEC driving control, construct a single photon detector with active quenching and fast recovery functions, and achieve automatic control of multichannel waveguide temperature using an equalization algorithm. Additionally, we develop a multichannel up-conversion single photon array detector with more uniform detection efficiency, greatly reducing initial manpower investment and avoiding errors caused by human factors.