With the development of artificial intelligence technology, the future water traffic environment will present a new pattern of coexistence of manned ships and unmanned ships, because unmanned ships are different from manned ships in situation understanding, collision avoidance decision-making, and so on. Therefore, the obstacle avoidance planning between unmanned ships and manned ships becomes extremely complex, and collision avoidance behavior scheme deduction becomes a key step in solving the problems related to situation understanding and collision avoidance decision-making in collision avoidance scenarios. In this paper, the situation understanding of the pilot for different collision avoidance situations is integrated into the dynamic obstacle avoidance model, and an intelligent navigation collision avoidance system is proposed to assist in deducing the collision avoidance action plan of the unmanned ship in the man–machine coexistence scenario. The intelligent navigation collision avoidance system is divided into two parts, namely a ship situation understanding part and a ship obstacle avoidance part, wherein ship situation understanding is used for realizing the transition of the collision state of the unmanned ship in the deduction process by constructing a collision-state set and a behavior decision set by using a finite state machine (FSM). Regarding ship obstacle avoidance, ship velocity obstacle is calculated based on the reciprocal velocity obstacle method (RVO), and the collision avoidance action is selected by using the behavior decision generated by the FSM to realize the dynamic collision avoidance deduction of the unmanned ship. In this study, the validity and effectiveness of the intelligent navigation collision avoidance system proposed in this paper are verified by case studies in a variety of collision avoidance scenarios. The system successfully solves the problem of intelligent collision avoidance planning, provides reliable support for the intelligent collision avoidance of unmanned ships, provides a feasible solution for safety and efficiency in sea navigation, and provides a valuable reference for the design and development of future intelligent navigation collision avoidance systems for ships.