While climate change is one of the greatest environmental threats the entire world faces today, rapid urbanization is making both the community and ecosystem more vulnerable to the impacts of climate change. Estimating urban resilience is thus one of the important processes to understanding the current and potential future risks of cities providing practical policies and qualified strategies to cope with climate change effects. This study presents a disaster risk analysis in Southern Taiwan at the municipal and zone levels using the Climate Disaster Resilience Index (CDRI). The index was estimated at both the zone and city scale of three coastal cities, namely Tainan, Kaohsiung, and Pingtung. The CDRI approach consists of five different dimensions (physical, social, economic, institutional, and natural), with several parameters and variables reflecting the abilities, strength, and threats of case study cities to cope with potential climate-related disasters. The findings show that, while the physical dimension has the highest resilience among cities, the lowest average scores and the least resilience belong to the natural dimension. The overall CDRI score for different cites also revealed various capabilities, shortcomings, drawbacks, and potential risks of neighbored cities in the same region. It is expected that the findings of this study shall serve as an urban planning tool to recognize the sectors within an urban context that are more or less resilient, enhance actions at the local level, and support future planning decisions.