In general, the wavelength of the projected laser in a laser system is a bit different from the beacon wavelength used for target acquisition and tracking. So the dispersion influence of atmospheric refraction in the horizontal transmission path should be considered to reduce calibration errors of the optical axis. Firstly, the relationship between dispersion effect of horizontal atmospheric refraction and various practical parameters, such as vertical temperature gradient, vertical pressure gradient, laser wavelength and laser transmitting distance, is deduced by theoretical analysis. Then the calibration errors of optical axis caused by dispersion effect of horizontal atmospheric refraction in the near surface layer is also analyzed. Furthermore, atmospheric temperature and pressure of varying height are measured by means of two automatic meteorological stations. And the calculation results show that the dispersion effect of horizontal atmospheric refraction in the near surface layer for 1 km transmission could be about 3 μrad for 1 μm and 5 μm wavelengths, which would lead to calibration errors of about 1.5 μrad. It indicates that dispersion effect of horizontal atmospheric refraction in the near surface layer should be monitored in order to reduce theoptical axis calibration error, and the optical axis calibration should be carried out when dispersion effect is slight enough.