A cover sterilizing mechanism for bottle filling device includes a sterilizing chamber (II) in which a cover sliding passage (102) is arranged. A cover blocking mechanism which will periodically hold the cover (94) to stay on the sliding passage (102) for a certain time, and multiple groups of nozzles (62) corresponding to the place in which the cover (94) is held on the sliding passage(102) are also arranged in the sterilizing chamber (II). The cover sterilizing device can uniform the sterilizing time of each cover, conduce to install covers orderly and improve efficiency of the bottle filling device.