Recently, reducing underwater radiated noise (URN) of ships has become an environmental issue to protect marine wildlife. URN of ships can be predicted by various methods considering its generating mechanism and frequency ranges. For URN prediction due to ship structural vibration in low frequency range, the fluid-structure interaction analysis technique based on finite element and boundary element methods (FE/BEM) is regarded as an useful technique. In this paper, URN due to a double bottom-shaped structure vibration has been numerically investigated based on a coupled method of FE/BEM to enhance the prediction accuracy of URN due to the vibration of real ship engine room structure. Acoustic radiation efficiency and URN transfer function in case of vertical harmonic excitation on the top plate of double bottom structure have been evaluated. Using the results, the validity of an existing empirical formula for acoustic radiation efficiency estimation and a simple URN transfer function, which are usually adopted for URN assessment in initial design stage, is discussed.