A microreactor is a chemical reaction device that mixes liquids in a very narrow channel and continuously generates reactions. They are attracting attention as next-generation chemical reaction devices because of their ability to achieve small-scale and highly efficient reactions compared to the conventional badge method. However, the challenge is to design a control system that is tolerant of faults in some of the enormous number of sensors in order to achieve parallel production by numbering up. In a previous study, a simultaneous control system for two different temperatures was proposed in an experimental system that imitated the microreactor cooled by Peltier devices. In addition, a fault-tolerant control system for one area has also been proposed. However, the fault-tolerant control system could not be applied to the control system of two temperatures in the previous study. In this paper, we extend it to a two-input, two-output fault-tolerant control system. We also use a fault detection system that combines ChangeFinder, a time-series data analysis method, and One-Class SVM, an unsupervised learning method. Finally, the effectiveness of the proposed method is confirmed by experiments.