Ecological suitability evaluation for hydropower development is effective in locating the most suitable area for construction and emphasizes a clear direction for water resources governance. In this paper, water footprints and transportation connectivity were introduced to improve the existing ecological suitability evaluation application for hydropower development by revising the defects of the traditional indicator system. The following conclusions were reached. (1) Tibet was in a state of water use surplus; the prospect of further hydropower development is positive. (2) Chamdo, Lhasa and Nyingchi excelled in water use efficiency, and Ali was placed last. Nakchu was slightly superior to Ali, but it lagged behind the southern regions. Lhasa, Chamdo, Nyingchi, Xigaze and Shannan were suitable for hydropower development, which could further meet local needs and benefit other regions of China. (3) The evaluation results were in accordance with the actual eco-environmental conditions of the built hydropower projects, indicating that current hydropower development planning was basically reasonable.