Aiming at the fault occurrence of AUV formation members during sailing, a fault tolerance algorithm of AUV formation based on reconfiguration was proposed. Firstly, the cost matrix is designed based on the reconfiguration and Hungarian algorithm to solve the problem of assigning target points under the fault condition. Then, based on Bezier curves, the dynamic constraints of AUV are designed parametrically. The nonlinear optimization problem satisfies the constraints through the characteristics of spline curves, and the adaptive particle swarm optimization algorithm is used to solve the tracking trajectory. The comparison and simulation experiment of a particle swarm algorithm based on a reconfiguration map (RMPSO) was carried out. The simulation results show that under the same planned path, the total tracking path of the following AUV is shorter, the turning radius is smaller, and the heading Angle is more stable. Finally, field tests are carried out in Qiandao Lake to verify the effectiveness of the algorithm for formation faults.