Abstract: The ecological space protection pattern and its connectivity play an important role in maintaining local biodiversity. This study is based on the spatial utilization management of theYangtze River Estuary (YRE) in Shanghai, and uses morphological spatial pattern analysis (MPSA) and landscape connectivity models to study the habitat characteristics of the YRE based on the spatial management model of the sea area. It identifies important ecological source areas and their connectivity and analyzes their compatibility with the existing protection pattern in order to contribute to the integrated protection of the YRE. Results indicate that there are 12 main ecological source areas in the YRE, with a total area of approximately 3080 km² accounting for 28.6% of the areas of Shanghai’s Marine Functional Zoning. The important source areas are mainly located in the southern branch of the YRE and the nearby sea area with 23 ecological corridors connecting 12 ecological source areas. The ecological source space identified in this study matches well with the latest marine ecological protection red line space announced. However, the important protection space is insufficient outside the river mouth, especially in important protection space near the southern and northern branches.