Aiming at the detection of low-flying small target within sea clutter, a hybrid algorithm of Kirchhoff Approximation(KA) and Method-of-Moments(MoMs) is utilized for analyzing the Doppler spectrum signatures of low-flying small target located above rough sea surface. The effects of sea state parameters, incidence angles, the speed of flying target, the distance between the target and the sea surfaces, the shape of the target’s cross-section on Doppler spectrum signatures of backscattered echoes from time-varying sea surface are investigated in detail. This study is of great importance for the analysis of coupling scattering mechanism between sea surface and the target above it as well as for the detection and identification of low-flying small target within sea clutter.