Nanostructures stripe deposition technique is a new method to develop nanostructures length standard transmission with the near resonance laser wave field manipultaion in neutral atoms. But all the information of nano-gratings deposited by laser standing wave field can not be given only through the one-dimensional or two-dimensional. The semi-classical model is used to simulate the three-dimensional trajectory and deposition distribution of the chromium atoms in the Gaussian laser standing wave field using the Runge-Kutta method from their motion equation in laser standing wave field. Then the three-dimensional deposition stripes are given, moreover, the effects of atomic beam divergence, chromatic aberration and spherical aberration on deposition structure are also analyzed. The study shows that results of three-dimensional simulation in Gaussian laser standing wave field of Cr can visually demonstrate the more detailed innate characters.