The work aims to solve the frequent positioning failure of EMS transport trolley in operation. An automatic cleaning device of EMS transport trolley positioning system was designed. Such device was composed of the cleaning mechanisms for positioning barcode and code reading head. Through the study on their key technologies, the design and relevant control parameters of the automatic cleaning mechanism of positioning barcode, electric push rod, automatic cleaning mechanism of code reading head and automatic cleaning control system, etc. were adjusted, so as to achieve the automatic regular cleaning of the positioning system and the code reading head. The automatic cleaning device could keep clean the EMS transport trolley positioning system. With such device, the shutdown caused by the positioning failure was eliminated, and the parking positioning accuracy reached 100%. The unattended operation of the EMS transport trolley system has been realized, which reduces the operation cost of EMS transport system. The device can also be used for the cleaning devices of such equipment as circular shuttle bus, stacker, movable turnover machine and barcode mover, etc.