A thruster reconfiguration control approach of manned submarine with 7000m operation depth based on quantum-behaved particle swarm optimisation (QPSO) is presented in this article. The manned submarine has eight thrusters. When thruster faults happen, the corresponding weight matrix is updated to restrict the usage of the faulty thruster. But the solution with this method may become unfeasible (exceed the rated valve of the thruster) and cannot be directly applied to the thrusters. In order to complete an appropriate control law reconfiguration, a novel control reallocation method based on QPSO is proposed. Not only is the solution obtained by the approach of QPSO limited in the whole feasible space, but also the control error of the fault-tolerant control is very small. Eight dimensions of the particles are used in this article, and each particle represents the components of the control vector, it searches in the range of the restricted factor value to make sure that all the reconfiguration control solutions are feasible. Compared to the weighted pseudo-inverse method, the error of the obtained control vector with the QPSO is very small. Finally, simulation examples of multi-uncertain faults are given to illustrate the advantages of the proposed method.