The Thelephora ganbajun is a rare edible mushroom which is distributed only in Yunnan area of China. It grows generally in the red soil under Burma pine. Therefore, there is a lot of dirt on the mushroom. The dirt adheres and embeds on the root firmly and deeply, thus to clean them is very difficult. The paper reports an efficient method to clean T. ganbajun using ultrasonic cleaner. The optimum parameters for ultrasonic clean are: detergent: 0.67%, sample:water=1:100, T=21.5-25.0 degrees C, and cleaning time: 20 min. Under the optimum condition, the cleaning efficiency can be increased 55.5% than that without sonication. Higher cleaning efficiency and more edible parts of the rare mushroom was got.