This paper deals with the problem of fault-tolerant control synthesis for underactuated marine surface vessels (MSVs) with dynamic uncertainties, external time-varying disturbances, and input saturation. In control design, with the help of neural networks (NNs) to reconstruct the dynamic uncertainty of the system, a novel nonlinear finite-time disturbance observer (FTDO) is established to reconstruct the compound uncertainty online, including unknown time-varying disturbances, approximation errors, bias faults and parts of loss-of-effectiveness (LOE) faults. Combining finite-time control (FTC) theory, event-triggered control (ETC) technology and backstepping design method, a new fault-tolerant control scheme for underactuated MSVs is designed. Based on the Lyapunov stability theory, it is proved that all signals in the closed-loop tracking system are bounded, and the tracking error of the underactuated MSVs converges to a small set near the origin in finite-time. The effectiveness of the proposed novel fault-tolerant control scheme is verified by computer simulation.