The invention provides a permanent magnet fault-tolerant motor drive controller for thrust vector control. The controller includes a digital controller composed of a DSP and an FPGA, an isolated drivecircuit, a fault-tolerant power driver and a signal processing circuit. According to the drive controller, a Hall current sensor is used to collect the phase winding current of a motor, the positionand rotating speed signals of a motor rotor are collected through a rotary transformer, after the signals are processed by the signal processing circuit and are subjected to analog-to-digital conversion, digital signals representing a phase winding current value, a rotor position and a rotating speed are sent to the digital controller, the digital controller estimates the rotor position and the rotation speed of the motor in real time through a sensorless control method based on non-orthogonal two-phase winding high-frequency injection according to a non-fault two-phase winding current signalof the motor, which is in mutual dissimilarity redundancy with motor rotor position and speed signals obtained by a mechanical sensor, and the reliability of the motor position detection is improved.The controller has good fault isolation ability and fault-tolerant running performance and high power density, and the drive control requirements of high reliability, high power density, and high servo performance of a thrust vector control system in the aerospace field can be effectively satisfied.