The South Island Line (East) will be a medium capacity railway comprising underground and viaduct sections. A medium capacity system with 3-car trains requires shorter platforms and smaller stations, while maintaining a similar train frequency to other MTR lines which generally use 8-car trains.

The railway will be underground except for the section between the Aberdeen Tunnel toll plaza and Ap Lei Chau which will be on a viaduct. The viaduct design has been enhanced to use slender and rounded viaduct columns and harmonious colours for the viaduct facade and noise barriers, to better integrate with the surrounding environment. Landscape works under the viaduct will create new open spaces for the public.