Distributed electric propulsion (DEP) aircrafts have high propulsion efficiency and low fuel consumption, which is very promising for propulsion. The redundant thrusters of DEP aircrafts increase the risk of fault in the propulsion system, so it is necessary to study fault-tolerant control to ensure flight safety. There has been little research on coordinated thrust control, and research on fault-tolerant control of the propulsion system for DEP aircrafts is also in the preliminary stage. In this study, a mathematical model of DEP aircrafts was built. Aiming at the lateral and longitudinal control of DEP aircrafts, a coordinated thrust control method based on total energy control and total heading control was designed. Furthermore, a fault-tolerant control strategy and control method was developed for faults in the propulsion system. Simulation results showed that the controller could control the thrust to the prefault level. The correctness and effectiveness of the designed coordinated thrust control method and the fault-tolerant control method for DEP aircrafts were theoretically verified. This study provides a theoretical basis for future engineering application and development of the control system for DEP aircrafts.