A method for forming a semiconductor device structure is provided. The method includes performing a first process over a surface of a semiconductor substrate. The method includes forming a protective layer over the surface of the semiconductor substrate in a first chamber after the first process. The method includes performing a first transferring process to transfer the semiconductor substrate from the first chamber into a substrate carrier. The method includes performing a second transferring process to transfer the semiconductor substrate from the substrate carrier into a second chamber. The semiconductor substrate is located in the substrate carrier during a substantially entire first time interval between the first transferring process and the second transferring process. The method includes removing the substantially entire protective layer in the second chamber. The method includes performing a second process over the surface of the semiconductor substrate.