The present invention relates to a filling device of plant culture medium, which comprises two flow control valves, and each of the flow control valves is connected with a material delivery pipe and simultaneously connected between a waste discharge pipe and a filling pipe. When each of the flow control valves is switched to a cleaning position, the material delivery pipe and the waste discharge pipe are communicated with each other, but not with the filling pipe. Therefore, the material delivery pipe may be injected with a cleaning fluid for sterilization and cleaning, and the cleaning fluid will be drained through the waste discharge pipe after flowing through the material delivery pipe. When each of the flow control valves is switched to a filling position, the material delivery pipe and the filling pipe are communicated with each other, but not with the waste discharge pipe. Therefore, the material delivery pipe may be injected with a plant culture medium, such that the plant culture medium may be proceeded with the filling operation through the filling pipe.一種植物培養基之充填裝置的操作方法,主要是當各流向控制閥切換至一清洗位置時,輸料管與廢料排放管之間相互連通,但與充填管之間互不相通,因此可對輸料管注入一清潔流體來進行滅菌及清洗,待清潔流體通過輸料管之後再從廢料排放管排出,當各流向控制閥切換至一充填位置時,輸料管與充填管之間相互連通,但與廢料排放管之間互不相通,因此可對輸料管注入一植物培養基,使植物培養基藉由充填管來進行充填動作。10‧‧‧充填裝置20‧‧‧流向控制單元22‧‧‧第一流向控制閥24‧‧‧第二流向控制閥30‧‧‧廢料排放管40‧‧‧充填管50‧‧‧輸料單元52‧‧‧第一輸料管54‧‧‧第二輸料管