Based on laser focused Cr atom beam deposition, the simulations of effect of substrate diffraction on evolution of the atom wave-packet probability density in the focused laser standing wave are done with scalar optical diffraction theory. The results show that such effect will vary with parameter b0 which stands for the distance between laser axis and substrate surface which is used for deposition. Compared with non-diffraction, the central value of the probability density distribution of the atom wave packet at the focal plane will be increased and its FWHM will be reduced by substrate diffraction. When b0=－0.2w0, the focal plane of the atom wave packet coincides with substrate surface, and the probability density distribution of the atom wave packet has central value of 1.26 with FWHM of 5.62 nm under diffraction, which are 1.1 times and 0.94 times of that without diffraction, respectively.