In the study of electromagnetic scattering of multi-target composite on and above the rough sea surface, the common algorithm such as the method of moment analyzes the relationship between the target and the rough sea surface point by point, so the common algorithm usually requires massive computation and a lot of time. In this paper, the rough sea surface is described by Pierson-Moscowitz (PM) spectrum and Monte Carlo method, and the composite electromagnetic scattering from multiple conductor flying targets above the rough sea surface is investigated by using the hybrid algorithm-the method of moment in the Kirchhoff approximation. The composite scattering region is divided into target region and rough sea surface region. The target region and the rough sea surface region are investigated by using the method of moment, and the Kirchhoff approximation, respectively. The formulas of the hybrid algorithm in different polarizations are derived in detail, and the scattering coefficients in different incident angles, target heights, target sizes, target distances and wind velocities are calculated in detail. The characteristics of the composite scattering coefficient from the multiple conductor flying target above the rough sea surface are also obtained. Results show that the hybrid algorithm, i. e., the combination of method of moment and the Kirchhoff approximation, can obtain higher accuracy, and reduce the computation time efficiently. The computation time used by the hybrid algorithm is 19% of that by using the method of moment. Moreover, the performance becomes more favorable with the increase of size of rough sea surface.