An apparatus for controlling line guide of an automated material handling system, comprises: optical lines in which a side light emission optical fiber is installed in the whole section of a confluence of a plurality of lines of lines for moving the unmanned transport devices; a main confluence control device which is installed at the confluence, performs optical communication with the unmanned transport device through the optical line; and a sub-confluence control device which is installed in the unmanned transport device, performs optical communication with the main confluence control device through the optical line to report an entry state or a pass completion state for the confluence, and controls the unmanned transport device to perform an entry operation or a standby operation depending on the pass control signal.