Abstract: In this paper, a mathematical model for quantitatively analyzing Shack-Hartmann wavefront sensor(S-H WFS)'s detecting error under realistic atmospheric turbulence is presented, and the transfer characteristics of a variety of detecting error are researched. Results show that the S-H WFS's detecting errors will increase due to the atmospheric scintillation, sky background radiation and so on when Shack-Hartmann wavefront sensor is used in probing very low light level beacon, and along with the decrease of the contrast between the beacon and the sky background, the centroid detecting error goes up while the aperture input fluctuates more strongly.