To control the diffraction of a target illuminated by a radar wave, one technique is to consider periodics metamaterials. When they are applied as very thin heterogeneous layers on the surface of the target, the simulation by a full wave method based on meshed model has to deal with a multiscale problem, resulting in a huge amount of unknowns. This paper proposes to apply the metamaterial as an equivalent boundary condition via the Leontovich formula. The frequency-angle-polarizationdependent model is integrated on the surface target with a conformal FDTD resolution method. To establish the surface impedance model, a pattern of the metamaterial is modelled with periodic boundary conditions. The Spectral FDTD scheme is retained because existing numerical models developed for the FDTD method can be easily adapted to this method. Then, the CFL condition of the Spectral FDTD method is not restrictive and is the one given by the standard Yee scheme. The accuracy of the new scheme is first compared with the full material FDTD meshing and the Cartesian SIBC model when the target is a plate or a cube. Finally, the computational efficiency of the proposed SIBC model is evaluated on a cylinder with comparisons between FEKO, CST software and our homemade solver.