A film deposition system includes a substrate carrier, a film deposition device, a transport device and a cooling device. The substrate carrier includes a carrier body that defines an isolated space therein, and a phase transition material that is filled into the isolated space and that has a melting point ranging between 18° C. and 95° C. The phase transition material is capable of absorbing thermal energy from the carrier body as latent heat to change the phase of the phase transition material from solid to liquid. The cooling device is configured to absorb thermal energy from the substrate carrier so as to change the phase of the phase transition material from liquid to solid.