This study aims to estimate ship collision risk considering the occurrence frequency and severity simultaneously, as well as to explore the influence of ship domain shapes on estimation results in the Yangtze River estuary waterway. In contrast to the circular ship domain, the elliptical domain may result in an overestimate for head-on collisions and overtaking collisions, while it may underestimate the small-angle and large-angle crossing collision frequency. Conversely, the sector domain may underestimate the occurrence frequency of all collision types. Results also reveal that overtaking encounters are the most common type with a relatively low severity degree, while large-angle crossing collisions are associated with a lower frequency but a higher potential for causing serious consequences. The collision occurrence likelihood and severity are a little higher for the passenger ship type. Furthermore, two high-risk areas are found to be located between longitudes of 121°33′E and 121°46′E, 121°50′E and 121°58′E, respectively. The results of this study are beneficial for a better understanding of the overall collision risk in the Yangtze River estuary waterway.