To analyze the effects of different clean-processing on the quality of taproot，scissor and tendon of Radix Notoginseng and provide reference for better clean-processing of Radix Notoginseng.Methods:According to the present condition of clean equipment，we developed five kinds of cleaning methods to process the Radix Notoginseng，including ultrasonic cleaning 5 min，ultrasonic cleaning 10 min，rinsing，filing，and water immersion in this study.Aim to confirm whether the quality of the Radix Notoginseng changed after the processing using the method we developed，we systematically analyzed the exterior characters，water content，total ash and the effective ingredients extracted by the methanol，saponins content of Radix Notoginseng，all of which were also quality control standard described in the Pharmacopoeia of the People's Republic of China (2015 edition).Results:Ultrasonic cleaning for 5 min were more suitable for the retention of roots and rootlets，both of filing and ultrasonic cleaning 5 min were good at rhizomes.The contents of methanol soluble extracts and saponins content of Radix Notoginseng were all according with rhizomes>roots>rootlets.Conclusion:This result suggested that dividing the Radix Notoginseng into different tissue and using the corresponding cleaning method are the effective way to keep Radix Notoginseng clean with a higher quality in the clean-processing.