This paper presents a fault-tolerant control for the trajectory tracking of autonomous underwater vehicles (AUVs) against thruster failures. We formulate faults in AUV thrusters as discrete switching events during a UAV mission, and develop a soft-switching approach in facilitating shift of control strategies across fault scenarios. We mathematically define AUV thruster fault scenarios, and develop the fault-tolerant control that captures the fault scenario via Bayesian approach. Particularly, when the AUV fault type switches from one to another, the developed control captures the fault states and maintains the control by a linear quadratic tracking controller. With the captured fault states by Bayesian approach, we derive the control law by aggregating the control outputs for individual fault scenarios weighted by their Bayesian posterior probability. The developed fault-tolerant control works in an adaptive way and guarantees soft-switching across fault scenarios, and requires no complicated fault detection dedicated to different type of faults. The entailed soft-switching ensures stable AUV trajectory tracking when fault type shifts, which otherwise leads to reduced control under hard-switching control strategies. We conduct numerical simulations with diverse AUV thruster fault settings. The results demonstrate that the proposed control can provide smooth transition across thruster failures, and effectively sustain AUV trajectory tracking control in case of thruster failures and failure shifts.