In order to study the effect of substrate position on laser-focused Cr atom deposition, the simulations of optical potential of Gaussian laser standing wave, atomic trajectories and deposited lines are performed based on the perspective of atomic trajectory with different substrate positions in the focusing laser. Effects on the above three aspects are fully indicated by substrate position. In spite of diffraction by substrate, the optimal substrate position occurs when substrate surface coincides with the laser axis. At the optimal position, with diffractive laser, deposited lines have full width at half maximum (FWHM) 0.96 times and the center peak value 1.03 times of that deposited by non-diffractive laser. Further more, in spite of diffraction by substrate, the deposited lines along y direction perpendicular to the laser axis have monotone decreasing center peak values and monotone increasing FWHM with different values of y.