Due to the simplicity and high reliability, brushless dc (BLDC) motors are widely used in space application. High-reliability levels are the vital aspect for ensuring the long-term stable operation of the BLDC motor system, which is used in aerospace applications. The fault-tolerant control of the BLDC motor is of great importance for its continuous operating capacity even under the faulty situation. This paper proposes a fault-tolerant topology composed of an additional phase leg and a fault-protective circuit for the high-speed low-inductance BLDC motor. Based on the analysis of the overcurrent and overvoltage phenomenon after the switch faults, a novel fault isolation and system reconfiguration method is presented. The method can achieve safe isolation and reconfiguration to avoid the secondary fault caused by direct switch of the redundant switch and the faulty switch after the fault-diagnosis process. Both simulation and experimental results confirm the feasibility and effectiveness of the proposed method.