The invention provides a fault diagnosing and tolerance control method for aircraft three-dimensional movement. The method comprises the following steps of according to a model and a state combination index discriminant when an aircraft has no fault, carrying out the fault diagnosing; and when the aircraft has a fault, firstly, classifying the fault, analyzing the influence of the whole-aircraft parameters and the flight dynamic properties according to the determined fault type, and remodeling an abrupt-change system after the fault occurs, so as to obtain a new model description when the aircraft has the fault. The design method of a tolerance controller is characterized in that the output of a fault-free model can meet the requirements of military standards by the designed control amount; and when the aircraft has the fault, the new model output is stable by the control input which is formed by the control amount and the non-artificial additional control amount caused by the aircraft fault.