This paper presents the finite element algorism and a method for resolving the dynamic interaction between structures (stakes, tubes, plates, peels) and coral foundation under the dynamic load. The authors have used two kinds of problems: a plane problem for stakes, tubes, plates and a space problem for peels constructions. The one way interaction of coral foundation (only compress not pull) have been simulated using the 2D and 3D element contacts. A system of nonlinear dynamic equation has been solved by the direct integration Newmark and iteration Newton-Raphson. The computations are executed in Matlab algorithm. The obtained results present here can be used as references for researches, computations and designs of marine constructions in coral foundation under the natural loads as: exploding waves, wind waves, tsunami, and defending and marine economic activities.