In this paper, the composite electromagnetic scattering problem of 3D double cubic above a 2D rough surface is analyzed by the hybrid MOMKA method, which combines the moment(MOM) methods and the Kirchhoff approximation (KA). The composite Electromagnetic scattering model of doubletarget above randomly rough surface is constructed, and the target is divided as MOM region while the rough surface is divided as KA region, the current on the rough surface is obtained through the KA approximation, and construct integral equation on the surface of target so as to get the current on target. The scattering field contains the interaction between the target and the sough surface. The efficiency and the convergence of this hybrid algorithm is numerical validated. By comparing the results with the conventional MOM, the validity and high efficiency of this method are verified. Then the scattering coefficients in different rms of rough surface, the different distance, height and size of target are calculated and discuss in detail.