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In this paper, an aluminum plate with a Peltier devices are used as a model. For the Peltier actuated thermal process is a nonlinear control affine system and the real system is usually contains fault owing to various factors, it is difficult to achieve excellent control consequent. In this paper, robust right coprime factorization is applied to analyse the thermal process. Then the derivation of the controller is also given for achieve robust stability and tracking performance. Finally, simulation and experimental results are presented to support the theoretical results.