Abstract: Due to the difference of wavelength in emitting laser and photoelectric tracking for high energy laser system, atmospheric turbulence becomes one of the factors affecting the pointing accuracy. Therefore, the purpose of this paper is to study the influence of atmospheric turbulence on pointing accuracy, and the angular deviation of axis between emitting laser and photoelectric aiming of the system was used to characterize the influence of pointing accuracy. First, atmospheric turbulence phase screen was constructed by Zernike polynomial method, and the model of laser propagation was established by using the theory of angle spectrum diffraction. Next, based on above two methods, the variations of angular deviation in distinct atmospheric turbulence and different tracking wavelength were simulated and analyzed. In the end, some related experiments were carried out to verify the results. It is shown that various tracking imaging wavelengths lead to different angular deviations under the equivalent turbulence conditions. For example, the closer the tracking imaging wavelength to the emitting laser wavelength is, the smaller the angular deviation is. Under the circumstance of the same tracking wavelength, angular deviation adds with an increase of turbulence intensity. The above results can provide important reference for improving the ability of damage of high energy laser system in engineering application.