Abstract: A new fault tolerant control method is proposed for a sequential continuous system which includes two subsystems. The fault of either of the two subsystems can be diagnosed using the adaptive observer method. The controller reconfiguration can be carried out by the other faultless subsystem using the fault estimation information and other measured information, leading to the fault tolerant control of the sequential continuous system. If the fault in the subsystem can not be repaired or there is long time delay when the fault is compensated, traditional fault tolerant control methods of the complex systems can not be used. Fault tolerant control scope is extended by the proposed method. Computer simulation results illustrate the validity of the method.