Considering the dynamic positioning (DP) vessel control system with actuator faults and unknown environment disturbances, a fault-tolerant control scheme based on improved iterative learning observer (ILO) is proposed in this article. Firstly, the kinematics and dynamics models of DP vessels are established containing the actuator faults and environmental disturbances. Secondly, an improved ILO is designed to handle the unknown faults and disturbances concurrently with higher estimation precision by introducing the state information of the previous moment. Further, a prescribed-time active fault-tolerant control scheme is presented on the basis of the improved ILO and prescribed-time stability. And the stability of proposed ILO and DP fault-tolerant control system are analyzed based on Lyapunov theory. Finally, the effectiveness and advantages of the presented ILO and active fault-tolerant control scheme are illustrated by numerical simulations and comparisons.