Aiming at the problem that the permanent magnet of the six-phase permanent magnet synchronous motor (SP-PMSM) is prone to demagnetize under complex operating conditions, a reconstruction method of permanent demagnetization fault is proposed based on the super-twisting algorithm. Firstly, the mathematical model of the demagnetization fault for SP-PMSM is constructed based on the vector space decomposition (VSD) theory through order reduction and decoupling. Secondly, taking the stator current as the state variables, the sliding-mode observer is designed using the super-twisting algorithm. The real-time reconstruction of rotor flux is realized according to the principle of sliding mode equivalence. A kind of strong quadratic Lyapunov function is used to ensure the stability of STA-SMO. Finally, the simulation and experimental results demonstrate the effectiveness of the proposed method. Compared with the traditional sliding mode observer (SMO), the STA-SMO can reconstruct the demagnetization fault accurately, reduce chattering effectively and has a good robustness.