This study integrated coastal-watershed models and combined a risk assessment method to develop a methodology to investigate the impact resulting from coastal disasters under climate change. The mid-western coast of Taiwan suffering from land subsidence was selected as the demonstrative area for the vulnerability analysis based on prediction of sea level rise (SLR), wave run-up, overtopping, and coastal flooding under the scenarios of 2020 to 2039. Database from tidal gauges and satellite images were used to analyze sea level rise using EEMD (Ensemble Empirical Mode Decomposition). Extreme wave condition and storm surge were estimated by numerical simulation using WWM (Wind Wave Model) and POM (Princeton Ocean Model). Coastal inundation was then simulated via WASH123D watershed model. The risk map of study areas based on the analyses of vulnerability and disaster were established using the AHP (Analytic Hierarchy Process) technique. Predictions of sea level rise, the maximum wave condition and storm surge under the scenarios of 2020 to 2039 are presented. The results indicate that the sea level at the mid-western coast of Taiwan will rise in an average of 5.8 cm, equivalent to a rising velocity of 2.8 mm/year. The analysis indicates that Wuqi, Lukang, Mailiao, and Taixi townships are susceptive, low resistant and low resilient, and reaches the high risk level. The assessment provides that important information for making adaption policy in the mid-western coast of Taiwan.