A novel three-dimensional semi-vectorial beam propagation method based on the variable transformed galerkin method(3D-VTGM-SBPM) is proposed for directly modeling optical waveguides,and is successfully applied to simulate parallel directional coupler. By adopting proper variable transformation,the basic three-dimensional semi-vectorial BPM equations is reduced to a first-order normal differential equation system. The artificial boundary condition is avoided,and the polarization characteristic of the mode field is displayed.