Hydrodynamic analysis of a floating multi-body pier interacting with incident waves is carried out in the present research and results of wave-induced motions and structural responses are described. The objective is to develop a procedure which can be used to analyze the motions of such a floating structure consisting of a number of rigid pontoons linked together. Also, optimization of pontoons geometry for a desired length of the pier is examined. In this regard, different alternative arrangements of pontoons with different numbers and dimensions are studied and dynamic responses of these alternatives are investigated. Analysis of the multi-body floating structure is carried out in the frequency domain. The wave-induced forces and the responses are computed by three-dimensional diffraction method. To examine the effect of using different pontoons on pier hydrodynamic response, motion-amplitude transfer functions (RAO) and connector forces for a wide range of wave frequency and heading angle are computed. Results include the absolute and relative responses of the individual pontoons and prediction of pier motions for a wide variety of pontoon geometries in different wave frequencies and heading angles. Also results include effects of pontoons dimension on the response of structure and present heave, roll and pitch motions for floating pier structural system.