Recently, there are many studies about shortening frequency and increasing strength of storm surge due to worldwide climate change. Many studies emphasize that “super typhoons” will arrive in Korea in a few year. Because storm surge is very closely linked with super typhoon, so Korea can not be a free country any more. From this background, this paper evaluated damages from 30, 50, and 100-year frequency storm surges using MD-FDA(Multi-Dimension Flood Damage Assessment). Using this results and government’s port disaster prevention facilities costs, this paper also suggested the economic feasibility studies for Mokpo and Masan ports area. The B/C ratio for Mokpo is 2.95 and that of Masan is 1.28, the economic feasibility of both ports are very high. This paper can be used to make a guide line for government’s preliminary feasibility study for the port disaster prevention systems.