From the perspective of motor control and manufacturing process, the application of faulttolerant permanent magnet rim driven motor (FTPM-RDM) in shaftless rim driven thruster (RDT) can avoid complicated shafting structure in traditional propulsion system effectively and realize sensorless control while reducing volume. Referring to fault-tolerant structure features, this paper introduces an improved sensorless control algorithm based on two-stage second-order generalized integral (SOGI) pulsating high-frequency (HF) voltage injection which is applied to the FTPM-RDM in zero and low speed. This algorithm can realize the rotor position estimation under fault and healthy condition. Based on pulsating HF injection method, HF square-wave voltages are injected in the virtual dq axis, and the initial rotor position can be extracted from the response currents of stationary reference frame (SRF). The sinusoidal voltage is injected into the virtual dq axis, and use two-stage SOGI instead of the traditional filter is used to realize the current modulation without delay in low speed rotor position estimation. Combining the simulation and experiments, the proposed sensorless control strategy can estimate the rotor position accurately whether in failure or not and has good dynamic and static performance.