The dynamic response of caisson structure with suction force between bottom of caisson and seabed was numerically evaluated in the frequency domain by means of structureseabed interaction analysis. In this paper, caisson structure was assumed to be a rigid rectangular prism with skirt, whose base has several square compartments, and the suction force was to act on each compartment. While the seabed was assumed to be a fluidsaturated poroelastic medium whose behavior is governed by Biot's theory of wave propagation. The effects of skirt length of caisson structure and suction force type acting on compartments on the dynamic response of caisson structure were numerically investigated.