The modern optical systems have placed stringent requirements on the manufactures and measurements of optical elements. Measurement accuracy of nanometer is needed. Phase-shift point diffraction interferometer is a common instrument in high-accuracy measurement, whose reference wave is generated by a pinhole with diameter of several hundred nanometers. So the measurement accuracy can be estimated by analyzing the diffracted reference wave. A two-dimensional simulation, based on finite element method (FEM), is set up to study the propagation of the visible light of 632.8 nm wavelength, through sub-1000 nm diameter pinholes in a chromium membrane with different thicknesses. Beam spot alignment error and tilt are also analyzed.