This paper develops a model-based control system for fault detection and controller reconfiguration using stochastic model predictive control (MPC). The system can determine online the optimal control actions, detect faults quickly, and reconfigure the controller accordingly. Such a system can perform its function correctly in the presence of internal faults. A fault detection model based (FDMB) controller consists of two main parts: the first is fault detection and diagnosis (FDD) and the second is controller reconfiguration (CR). Systems subject to such abrupt failures are modeled as stochastic hybrid systems with variable-structure. This paper deals with three challenging issues: design of the fault-model set; estimation of hybrid multiple models; and stochastic MPC of hybrid multiple models. For the first issue, we propose a simple scheme for designing a fault model set based on random variables. For the second issue, we consider and select a fast and reliable FDD system applied to the above model set. Finally, we develop a stochastic MPC scheme for multiple model CR with soft switching signals based on the weighted probabilities of the outputs of different models. Simulations for the proposed FDMB controller are illustrated and analyzed. © 2011 John Wiley and Sons Asia Pte Ltd and Chinese Automatic Control Society.