Using neutral chromium atoms for the fabrication of nanometer-scale ordered structures is a new method of generating nanostructures on a substrate. But all the information of nano-gratings deposited by laser standing wave field can not be given only through one-dimensional or two-dimensional analysis. Three-dimensional analysis of the effects of atomic beam divergence angle on the process of fabricating nano-grating was discussed based on the three-dimensional motion model of Cr atoms in Gaussian standing wave laser field. The study shows that the preparation of a high-collimated and transversely cooled atomic beam, typically under 0.6 mrad, is essential to minimize the severely disadvantageous effects for deposition of atoms in laser standing wave.