This article focuses on vulnerability in transportation systems because of large-scale disasters. We proposes an index of isolation vulnerability as a new metric for network vulnerability analysis. Isolation vulnerability covers the situation in which supporting bases and receiving bases in a network cannot connect when some links are degraded due to external forces imposed on the network. Isolation vulnerability is derived as a solution of the maximum flow problem for a one-to-one network extended for supporting bases and receiving bases. A single set of link combinations does not necessarily exist that defines an isolation vulnerability, i.e., a set that is isolation-critical. A method of enumerating all of these critical link sets is provided and applied to the road network in Sapporo city, Japan, to identify highly vulnerable public shelters and analyze their characteristics.