The development of traditional vehicles which consume fossil carbon-based fuels is constrained by environmental pollution and the energy crisis, and it has become a social consensus to develop electric vehicles with new energy resources and low emissions. The drive system of electric vehicles should be able to reliably operate over a long period. When a short-circuit fault occurs in the driving motor, the current in the winding will increase sharply and threaten driving safety. This paper proposed a short-circuit fault-tolerant control strategy for a dual three-phase permanent magnet synchronous traction motor (DT-PMSTM) which can resolve the problem of short-circuit faults. The current in non-short-circuit fault windings has been reconstructed to offset the interference of the short-circuit current and output a stable torque. Based on the principle of constant composited magnetic motive force (MMF), the dimension-reduced orthogonal transformation matrix was derived. The compensation currents were designed according to the interference effect of the short-circuit current to the normal MMF of the motor. Consequently, the lost torque component caused by the lack of the short-circuit winding was compensated, and the torque pulsation was also reduced. The performance of the topologies with neutral point-isolated mode and neutral point-connected mode were both investigated and compared. The validity of the proposed short-circuit fault-tolerant control strategy was proved by the simulation results.