A temperature control system was developed to save energy in freeze dryer. The objective part in the freeze dryer was a shelf with an electrical heater and cooling compressor. The shelf was a fluid circulation heat exchanger. The temperature control of the shelf is generally a feedback control by present and set values of the shelf temperature only, whereas in new control algorithm the circulating fluid temperature and fluid circulating speed were included as well. The control algorithm was based on a concept of refraining the heater and cooler from being in operation if unnecessary. Actuators in use were mainly thyristor for heater, relay for cooling compressor, inverter for fluid circulating pump, etc. Type of Interfaces were RS232C, and digital-analog converter and digital-output converter. Program language was Visual Basic 6.0. Finally, control performance by the new algorithm could be improved in terms of energy saving and accuracy.