Standing wave of laser light acts as an array of lenses to focus the moving atoms in atom lithography. The position between standing wave and substrate plays an important role in determining the quality of depositional nanometer lines. Using the rule of Gaussian beam, a method of accurately identifying the position of standing wave of laser light is reported. By adjusting accurately the displacement stage which carries the beam focus lens and reflective mirror, the laser beam is subsequently shielded by depositional substrate. Signal of photoelectric detector is changed because of shielding the standing wave, so we can convert the displacement of standing wave into electrical signal. Positioning the standing wave against substrate is achieved by using the value of waist diameter of standing wave of laser light. Theoretical model is developed according to the experimental process. The result of numerical computation coincides well with the experimental record. This method realizes accurately positioning standing wave of laser light against substrate, and it provides the experimental basic for deeply studying the influence of the distance between standing wave and substrate on the quality of depositional nanometer lines.