According to the traffic safety situation in the navigation waters of the Pearl River Estuary, the sub models of ship navigation density, traffic conflict and vector kinetic energy risk were established based on the dynamic ship domain and relevant calculation models, and by mining and analyzing accident data and ship dynamic data, additional risk weighting was carried out for special cargo ships that are prone to accidents. Then, four risk factors were coupled to establish a systematic risk assessment model for the navigation of the Pearl River Estuary. Finally, according to the realtime operation status of ships in the water area, the relevant calculation parameters were calibrated, and the “Pearl River Estuary navigation risk comprehensive index” was calculated by using the coupling model, and the risk index was divided into four levels. The verification analysis shows that the navigation risk assessment model is objective and practical, which can provide technical support for maritime supervision.