The operation of a brushless DC motor with dual-windings for the flight control system was described. The dual-channels electro-mechanical actuator (EMA) is composed of the motor, the fault-tolerance operation mode can be obtained when any channel is failure. The mechanical characteristic, power losses and allowed torque of the motor were analyzed at two cases of normal and fault-tolerance operation modes. From the experimental mechanical characteristics curve, it can be obtained that the no load speeds of two operation modes are same under the same voltage, but the speed drop in the case of the fault-tolerance operation is greater than the normal operation because of the load. Holding the power loss not changed in the case of fault-tolerance operation, the motorallowed current is 1.4 times of the rated current and the allowed torque is 0.7 times of the rated torque, these were validated by the temperature experimental data. The balance control of the dual-windings operation and the control method of the fault-tolerance operating were researched, the dynamic characteristic of the fault-tolerance operation was simulated.