The regional ship collision risk assessment for multiple ships in restricted waters is of great significance to the early warning of ship collision risk and the intelligent supervision of maritime traffic. Given the existed method of regional ship collision risk assessment without considering the impact of ship aggregation density, this paper proposes a novel regional ship collision risk assessment method that considers the aggregation density (AD) of the clusters of encounter ships (CES) for intelligent surveillance and navigation. The effectiveness of the proposed method has been examined by the experimental case study in the waters of Xiamen, China, and analysis has been compared with other existed studies to show the advantages of the new proposed algorithm. The results show that the study method can more intuitively and effectively quantify the temporal and spatial distribution of regional collision risks in the restricted sea area. The proposed method can improve the efficiency of traffic management when monitoring the ship collision risks in macroscopic view, and assist the safety of manned and unmanned ship navigation.