It is vital to analyze ship collision risk for preventing collisions and improving safety at sea. This paper takes Ningbo-Zhoushan Port, a typical complex navigable water, as the research object, propose a probabilistic conflict detection method to estimate the potential collision risk by using a dynamic domain model driven by AIS data. Combined with the algorithm of fast modularity optimization and spectral clustering, a ship group extraction method from the perspective of water navigation management was proposed. Aiming at ship traffic characteristics in complex navigable waters, conduct dynamic calculation of ship collision risk from individual, regional and local multi-scale perspectives. The results show that the proposed method can detect the collision risk in a timely, reliable and effective manner under complex dynamic conditions. As such, they provide valuable insights for ship collision risk prediction and the development of risk mitigation measures.