We investigate phonon transport properties of Si phononic crystals by using an atomistic Green function method. By varying form factors such as thickness, orientation, and pore size of unit cells, mean-free path and associated thermal conductivity of phononic crystals are obtained. We present the empirical formula for thermal conductivity as a function of cell size and, by extrapolating results from it for realistic cell sizes, the thermal conductivity is compared with experimental ones. The formula is found to predict a nearly equal amount of the suppression in thermal conductivity to the experimental values, implying a feasible calculation method for predicting thermal properties of phononic crystals