In Jeju province, the Citrus is widely spread crop which is the most popular fruit on the island. When the quality of a Citrus is not in a good condition or when its size exceeds or is lower than the set criteria, it is discarded as a waste. In this study, a drying machine for waste Citrus has been developed with 2.6 GHz microwave energy supply to the Citrus at vacuum environment. The vacuum environment of the drying chamber was maintained to reduce the energy supply to the Citrus by lowering the evaporating temperature of the water. The experiment was conducted with variation of the vacuum pressure, interior temperature of the drying chamber, and operating time of the microwave. As a result, the effect of the temperature was shown to be higher than the other two control methods, and it showed with 0.305 g/W evaporation efficiency.