A transport mechanism for a peripheral device and an operating method including the same are provided. The transport mechanism includes a tray, at least a transport roller, a detector, a trigger component and a processor. The tray includes an opening extending through the tray. The transport roller is rotatably installed in the opening and protruded from the tray to transport a flexible object to move along a transport path. The detector near the tray has a detecting area. The trigger component is located in the opening and spaced apart from the flexible object on the transport path. The flexible object deviated from the transport path presses the trigger component to enter or leave the detecting area and triggers the detector to transmit an abnormal detecting signal. The processor receives the abnormal detecting signal to stop the transport roller.