Disclosed is a heat treatment system for semiconductor devices. The heat treatment system is used in a heat treatment process for semiconductor devices, such as a crystallization process for an amorphous silicon thin film or a dopant activation process for a poly-crystalline silicon thin film formed on a surface of a glass substrate of a flat display panel including a liquid crystal display (LCD) or an organic light emitting device (OLED). The heat treatment system transfers a semiconductor device after uniformly preheating the semiconductor device in order to prevent deformation of the semiconductor device during the heat treatment process, rapidly performs the heat treatment process under the high temperature condition by heating the semiconductor device using a lamp heater and induction heat derived from induced electromotive force, and unloads the semiconductor device after uniformly cooling the semiconductor device such that the semiconductor device is prevented from being deformed when the heat treatment process has been finished. The heat treatment system rapidly performs the heat treatment process while preventing deformation of the semiconductor device by gradually heating or cooling the semiconductor device.