In this work, the finite element/boundary integral method (FE/BIM) combined with the domain decomposition method is introduced to study the electromagnetic scattering from the target above the rough sea surface. As the integral boundary can be set at anywhere with an arbitrary shape, the conformal truncated boundary is built to reduce the unknowns of the computational region combined with the domain decomposition method. In the interior region, the finite element method is used to solve the problem, whereas the artificial boundary condition can be obtained by the boundary integral method. The strategy of hybrid FE/BIM and the modeling method are presented with their validity evaluated by the method of moment, then bistatic scattering properties of a missile above the sea surface are discussed, and their dependence upon different incident angles, target height, wind speed above the sea, and the size of the missile are discussed in detail. The information of targets and the target detection can be retrieved and analyzed by the results in this paper.