In the past several decades, a great number of offshore structures have been constructed on loosely deposited seabed foundation because sometimes there would be no a dense seabed floor could be chosen in planned sites, for example, the breakwaters and oil platforms in the Yellow River estunary area, China. Wave-induced residual liquefaction is easy to occur in loosely deposited seabed, which brings great risk to the stability of offshore structures. In this study, we focus our attention on the 3D interaction mechanism between ocean wave, a caisson breakwater and its loosely deposited seabed foundation. A three-dimensional integrated numerical model FSSI-CAS 3D is taken as the computational tool; and the soil constitutive model: Pastor-Zienkiewicz Mark III (PZIII) proposed by Pastor et al. [16] is adopted to describe the wave-induced dynamic behavior of loose seabed soil. The numerical results indicate that the developed integrated numerical model FSSI-CAS 3D is capable of capturing a series of nonlinear phenomena, such as tilting, subsiding of breakwater, as well as residual liquefaction in loose seabed foundation etc., in the interaction process between ocean wave, a caisson breakwater and its loose seabed foundation. The purpose of this study is to provide coastal engineers with comprehensive understanding of FSSI problme involving loosely deposited seabed soil; and propose a reliable computational method to engineers involved in the design of offshore structures on loose seabed foundation.