Electro-Mechanical Actuator (EMA) is the core flight control system for aerospace aircraft. Due to the requirements of reliability and power density, multi-phase fault tolerant motor based integrated EMA has been the trend for next-generation actuator. Under fault mode, the stator windings of multi-phase motor can be rearranged with cutting off faulted channels to ensure safety and normal functions. However, fault-tolerant strategy brings about electrical parameter uncertainty and severe unbalanced force disturbance, leaving challenges for accurate servo control. In this paper, an adaptive robust controller is proposed to deal with uncertainty and disturbance in multi-phase fault-tolerant motor and enhance servo control accuracy. Firstly, the structure and operation principle of integrated EMA is introduced, especially focusing on the special structure of multi-phase motor. Based on that, the influence of fault tolerant strategy on electrical parameter and disturbance is analysed with accurate multi-phase motor model derived. Thus, the kinetic model of EMA system can be set up for controller design. In the adaptive robust controller, adaptive and robust items are designed respectively to solve uncertainty and disturbance problems. Finally, simulation of proposed controller is conducted in SIMULINK. Results show that proposed control strategy can effectively overcome parameter uncertain and enhance robustness under disturbance.