The increasing interest in marine mechatronic systems and their applications has promoted the development of advanced control algorithms for the trajectory control of marine vehicles including ships, surface vehicles, and underwater vehicles. In this paper, the finite-time fault-tolerant trajectory tracking of fully actuated marine vehicles is investigated in the presence of parametric uncertainties, external disturbances, actuator faults, and input saturation. A novel adaptive finite-time sliding mode control scheme is proposed by combining the homogeneous integral sliding mode manifold, the fast terminal sliding mode control, and the adaptation technique. Rigorous theoretical analysis for the practical finite-time stability of the whole closed-loop system is provided. The proposed control scheme can guarantee the position and velocity tracking errors converge to the small region about zero in finite time even in the presence of actuator faults. To the best of the authors’ knowledge, there are really limited existing controllers can achieve such excellent performance in the same conditions. In addition, the proposed control scheme is structurally simple, model-independent, and continuous with chattering free, which makes it affordable for practical applications. Numerical simulations illustrate the effectiveness and superiority of the proposed control scheme.