The port waterway network plays an important role in the organization and management of port ship traffic. Due to limited ship operations, conflicts, congestion, and safety issues often arise in port waters. Conflicts between ships can be predicted by collision detection between ships. A novel collision detection algorithm for trajectory pairs is proposed by introducing variable time interval variables. In addition, to improve the overall accuracy of trajectory compression and reduce redundant calculation in collision detection, a multi-factor Douglas-Peucker algorithm adapted to ship trajectory compression is proposed with the consideration of speed and turn constraints. The maximum speed difference of the algorithm is increased by 1.5–2.5%, and the average speed difference increased by 2.0–4.5%. Based on the method mentioned above, the risk assessment framework of maritime collision is established and the risk situation of the waters near Ningbo Zhoushan Port is evaluated and analyzed by using ship historical track data.