Coastal ecosystems are rich with biodiversity and ecological functions that provide valuable ecosystem services. They are also vulnerable to the impacts of climate change and anthropogenic activities. Assessing the impacts of climate change on coastal ecosystems is crucial if we are to develop and implement strategies that minimize and mitigate these impacts. This study uses a theoretical framework that includes climatic hazards, ecosystem vulnerability, and exposure to damaging climatic events, to estimate the risks due to climate change on coastal ecosystems in Taiwan. We found that seagrass beds, algal reefs, and coral reefs in Taiwan are at high ecological risk to the future effects of sea level rise, elevated sea temperature, and ocean acidification. The responses of these highly threatened ecosystems to the effects of climate change is uncertain and depend, in part, on the type of ecosystem, its location in Taiwan, the rate at which these effects occur, and whether these impacts occur at the same time or sequentially. The coastal ecosystem risk to the adverse effects of climate change is high because they are especially vulnerable. The resistance of coastal ecosystems is linked to their complexity and maturity. Their low adaptive capacity is linked to the exploitation of their natural resources and inadequate biodiversity conservation. To minimize and mitigate the effects of climate change on high-risk areas and ecosystems ongoing monitoring programs and dynamic management will be needed. Our study is a first step toward building a framework for climate change risk assessment for the coastal ecosystems in Taiwan.