The purpose of this study was to analyze the vibration characteristics of fuel cell vehicle assembled by support. Rubber mounts are a type of support made of rubber used for vibration isolation of structures. The dynamic properties of the isolator were measured by using beam-transfer function method. The modal characteristics of the fuel cell for vehicles were analyzed using a model that reflects the structural characteristics of fuel cell for vehicles. In order to verify the relationship between the dynamic properties of the rubber mount and the modal characteristics of the fuel cell, the mode shapes of the fuel cell according to stiffness of the isolator were measured. Finally, the modal characteristics of fuel cell were investigated to improve the durability of the fuel cell for vehicle.