Based on the nonequilibrium Green’s function formalism, we have developed a three-dimensional (3D) simulation framework capable of handling electronic transport in nanoscale silicon devices within the effective mass and Hartree approximations. Using the deformation potential theory and the self-consistent Born approximation, we obtain the spatially local self-energy functions for the intravalley and intervalley phonon scattering mechanisms. To make the 3D simulation practicable, we reduce the computational complexity by using the mode space approach suitable for the device whose cross section is relatively uniform along the transport direction. We also obtain the expression for the phonon-limited low field mobility in the long channel limit from the linear response theory. As an application, we study the quantum transport of the silicon nanowire transistor whose channel length is 15nm in the ballistic limit and in the presence of the electron-phonon interactions. We can observe various effects of the electron-phonon interactions such as the reduction of the drain current, broadening of the local density of states, and the energy relaxation of the electrons injected from the source.