Emergency responders in coastal cities are anticipated to provide effective evacuation of at-risk populations during the preparedness and response phases of coastal floods due to land-falling storms or cyclones. However, existing contingency plans primarily focus on the evacuation of the general public rather than special arrangement for elderly populations who constitute a large proportion of flood fatalities. Here we present a system-level methodology to elaborate citywide coastal flood evacuation plans for optimal deployment of shelters and effective transfer of elderly people with special needs. We conduct a comparative analysis between Shanghai and New York City, which are both among the most exposed coastal cities to storm-induced flooding but represent two distinct institutional systems of emergency operation. The results show marked disparities in evacuation patterns for elderly residents in the two cities. Storm flood evacuation is more challenging in Shanghai due to insufficient provision of shelter capacity (~230,000). Implementing risk-informed and strategic planning could not only meet the potentially huge demand of vulnerable elderly (~520,000) but also improve the overall efficiency of evacuee transfer by a factor of 3. Our work provides new insights into operational emergency evacuation decisions and informs flood management policy development for major coastal cities globally.