Global environmental changes have led to frequent occurrences of climatic extremes. The increasingly frequent and high-magnitude natural disasters in Taiwan have caused significant mortality, injury, and property damage. In response, there have been requests to improve the capacity to cope with extreme climatic conditions through increased awareness and identification of vulnerability. Disruptions to transportation systems affect the resilience for sustaining daily operations. Among the various types of transportation systems, ports provide substantial employment and industrial activity, contributing to national and regional development. In addition, ports integrate the functions of supply chains such as services in logistics, information, and business, becoming the location of industrial clusters. Therefore, this study examines the risk of port failures from the perspective of vulnerability. Specifically, seven vulnerable factors derived from the extant literature and lessons learned from the previous disaster cases are evaluated using geographic information systems. The results reveal that port capacity and efficiency have a significant effect on port vulnerability in which the efficiency of gantry cranes, labor productivity, free trade zone business volume, and ground access networks play crucial roles in port failure. Moreover, the risks associated with port operation are evaluated by overlapping a hazard map of areas prone to debris flows and tsunami inundation. The risk maps can assist decision makers in understanding the vulnerability and adopting appropriate strategies to minimize disaster risks.