We introduce a multi-domain decomposition Fourier finite element (MDDFFE) method for the simulation of three-dimensional (3D) marine controlled source electromagnetic measurement (CSEM). The method combines a 2D finite element (FE) method in two spatial dimensions with a hybrid discretization based on a Fourier FE method along the third dimension. The method employs a secondary field formulation rather than the total field formulation. We apply the MDDFFE method to several synthetic marine CSEM examples exhibiting bathymetry and/or multiple 3D subdomains. Numerical results show that the use of the MDDFFE method reduces the problem size by as much as 87 % in terms of the number of unknowns, without any sacrifice in accuracy.