An efficient wave energy converter with new overtopping flow device on which spiral reefs are attached is proposed by Maritime and Ocean Engineering Research Institute in Korea and its candidate substructures such as monopile, tripod and jacket are designed. This study investigates modal characteristics of the substructures by analyzing natural frequencies and mode shapes. Based on the modal analysis results, relative strength, governing modes and some complementary design strategies of each candidate substructure are compared and discussed considering water depth conditions.