A numerical approach to model the microwave emission from soil with vegetation cover is developed. The vegetation cover is represented as an irregular layer on top of a homogeneous half space representing the soil. The phase matrix of the layer components as well as the emission characteristics have been estimated using the Finite-Difference Time-Domain (FDTD) Method. The phase matrix was then integrated into a layer model that accounts for the scattering between the layer and soil, using the radiative transfer theory. The effects of interface roughness on emission are incorporated into the model through the surface phase matrices, which are computed using the Integral Equation Model (IEM). The validity of the phase matrices computation is tested against theoretical models. The microwave emission model predictions are compared to field measurements, showing a good agreement.