A transportation system of a cassette according to an embodiment of the present invention comprises a port and a system controller. The port accommodates a cassette carrying a glass substrate. The port includes a plurality of displacement sensors for sensing a position of a cassette. The system controller calculates a distortion amount of the cassette using a plurality of sensed values of the cassette and a misplaced amount of the displacement sensors to determine whether the cassette is in a normal settlement status. Therefore, the position of the cassette can be automatically taught without clamping operation of a clamping device clamping the cassette disposed in the port, so that it is possible to prevent defects of the glass substrate by removing various defect-causing factors such as particles and static electricity that may occur during a conventional clamping operation.