The RCA cleaning method is the industry standard way for cleaning silicon wafers, and the temperature control is important for a stable cleaning performance. However, the difficulty lies in the fact that the RCA solutions cause nonlinear and time-varying exothermic chemical reactions. So far, the MSPC (model switching predictive controller) using the CAN2 (competitive associative net 2) has been developed and the effectiveness has been validated. However, we have observed that the control performance, such as the settling time and the overshoot, does not always improve with the increase of the number of learning iterations for the CAN2. To solve this problem, we introduce the bagging method for the CAN2 and first-difference signals for effectively embedding the bagging method. The effectiveness and the performance of the present method are examined by means of numerical experiments.