An automatic pill picking system includes a base and a suction nozzle. The base defines a medicine port. The automatic pill picking system further includes a cleaning mechanism. The cleaning mechanism includes a pump, an inner pipe, and an outer pipe. A first end of the inner pipe is connected to the pump, and a second end opposite to the first end of that aims at inner side of the suction nozzle. A first end of the outer pipe is connected to the pump, and a second end of that aims at the medicine port. The inner pipe and the outer pipe are configured to blow off powder adhered to the suction nozzle when the pump blow airflow. The invention further discloses a cleaning method for the automatic pill picking system.一種自動取藥裝置,包括有一基座及一吸取藥丸之吸嘴,所述基座開設有一取藥口,所述自動取藥裝置還包括有清理結構,所述清理結構包括有幫浦、內接管及外接管,所述內接管一端連接所述幫浦,另一端對準所述吸嘴內部,所述外接管一端連接所述幫浦,另一端對準所述取藥口;所述吸嘴位於所述取藥口處,所述內接管及所述外接管於所述幫浦噴氣時吹除粘附於所述吸嘴上之異物。本發明還進一步揭露了一種應用於所述自動取藥裝置中之清理方法。90...清理結構40...幫浦41...出口50...過濾器51...進氣孔53...出氣孔60...轉接管61...接入端62...第一出口端63...第二出口端71...傳送管72...內接管73...外接管