This paper firstly adopts a fault accommodation structure, a five-phase permanent magnet synchronous generator (PMSG) with trapezoidal back-electromagnetic forces, in order to enhance the fault tolerance of tidal current energy conversion systems. Meanwhile, a fault-tolerant control (FTC) method is proposed using multiple second-order generalized integrators (multiple SOGIs) to further improve the systematic fault tolerance. Then, additional harmonic disturbances from phase current or back-electromagnetic forces in original and Park’s frames are characterized under a single-phase open condition. Relying on a classical field-oriented vector control scheme, fault-tolerant composite controllers are then reconfigured using multiple SOGIs by compensating q-axis control commands. Finally, a real power-scale simulation setup with a gearless back-to-back tidal current energy conversion chain and a small power-scale laboratory prototype in machine side are established to comprehensively validate feasibility and fault tolerance of the proposed method. Simulation results show that the proposed method is able to suppress the main harmonic disturbances and maintain a satisfactory fault tolerance when third harmonic flux varies. Experimental results reveal that the proposed model-free fault-tolerant design is simple to implement, which contributes to better fault-tolerant behaviors, higher power quality and lower copper losses. The main advantage of the multiple SOGIs lies in convenient online implementation and efficient multi-harmonic extractions, without considering system’s model parameters. The proposed FTC design provides a model-free fault-tolerant solution to the energy harvested process of actual tidal current energy conversion systems under different working conditions.