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Total ash clearance rates and saponins' loss rates of <i>Panax notoginseng</i> rhizome, root tuber, and rootlet all increased with a prolonged washing time and the rising of water temperature. Under the same conditions, the total ash clearance rates of fresh <i>P. notoginseng</i> were significantly higher than those dried. Meanwhile, the saponins' loss rates were opposite. The highest daily intake of bioavailability heavy metals was rootlet. However, all of that was significantly lower than the recommended daily intake, and both the target hazard quotients and hazard index values were lower than 1. Conclusion, it is effective to decrease washing time and water temperature in order to reduce the loss of saponins of <i>P. notoginseng</i> on the premise that ash content of Notoginseng conforms to standard of Chinese Pharmacopeias. Safety risk assessments of heavy metals based on bioavailability can further reduce the health risk of the heavy metal exposure of Notoginseng.<br>Practical applications: Notoginseng possesses the functions of hemostatic and promoting blood circulation. Clay on the surface of Notoginseng contains high content of heavy metal and induces the exceeding of standard. Washing is the most effective way to clean heavy metal attached on Notoginseng. However, research about the washing technology of <i>Panax notoginseng</i> is still blank. Heavy metals in Notoginseng that are taken orally are much higher than the amount actually absorbed by humans. In such a condition, the risk of heavy metals in Notoginseng will be overestimated, which may bring unnecessary loss to the development of Notoginseng industry. Therefore, this experiment researches the remaining of heavy metal under different washing water temperature and washing time. Also, we evaluate the bioavailability and risk of heavy metals in Notoginseng that are washed in an optimum condition. In this way, we provide technological parameters for the washing operation in processing <i>P. notoginseng</i> and referential data to set the quantity standard of heavy metal in Notoginseng.