A method for manufacturing a semiconductor device with a cobalt silicide film is provided in the present invention. The method includes the steps of providing a silicon structure with an interlayer dielectric formed thereon, forming a contact hole in the interlayer dielectric to expose the silicon structure, depositing a cobalt film on the exposed silicon structure at a temperature between 300° C.-400° C., wherein a cobalt protecting film is in-situ formed on the surface of the cobalt film, performing a rapid thermal process to transform the cobalt film into a cobalt silicide film, and removing untransformed cobalt film.