A stochastic functional approach (SFA) is developed to calculate electromagnetic composite scattering from a three-dimensional perfectly electric conducting (PEC) target on a randomly rough PEC surface. The stochastic Green's function for randomly rough surface is derived, and a novel four-path model is presented to describe the scattering mechanism of target-surface interactions. The SFA is used to obtain the difference scattering cross section due to the rough surface of target. As a simple example of a spherical target with rough surface, the SFA is numerically compared with other numerical approaches, showing its accuracy and effectiveness. Finally, the difference bistatic scattering from a complex electric large target with rough surface and its functional dependence on the parameters are discussed.