For photo resist processing in semiconductor manufacturing, the precise temperature control of wafer has been demanded to realize a more fine device in recent years. However, it is difficult to achieve the precise temperature control by a current wafer heating and cooling system, because the system cannot control the temperature of transient state including wafer movement from the nature of the system. An integrated heating and cooling plate was developed to overcome above problem. On the other hand, it is difficult to achieve the precise temperature control of the plate because of its mutual intervention and unstable non-steady heat conduction. For that reason, we propose the control system based on thermal model with finite element in this paper, which is the state feedback control with scheduled gain to the process progress. Moreover, we propose the in-process estimation of wafer temperature based on system identification. Experimental results illustrate the effectiveness of the proposed method and the arbitrary thermal history control of wafer.