Abstract: A method for transporting semiconductor wafers in semiconductor factory automation system, includes the steps of: a) processing a lot of semiconductor wafers to be contained in a semiconductor wafer cassette in a process equipment; b) sending a cassette transportation request from the process equipment to a cell management server when the process equipment has processed the lot of semiconductor wafers; c) generating a transportation instruction in response to the cassette transportation request; and d) if the semiconductor wafer cassette is transported from the process equipment to a stocker by an automatic guide vehicle (AGV), simultaneously activating the AGV and the stocker by simultaneously sending the transportation instruction to the AGV and the stocker. The method in accordance with the present invention can reduce a time taken to transport the semiconductor wafers.