Based on the residual turbulent scintillation theory, the Mie-scattering lidar can measure the intensity of atmospheric turbulence by detecting the light intensity scintillation index of the laser return signal. In order to evaluate and optimize the reliability of the Mie-scattering lidar system for detecting atmospheric turbulence, the appropriate parameters of the Mie-scattering lidar system are selected and optimized using the residual turbulent scintillation theory. Then, the Fourier transform method is employed to perform the numerical simulation of the phase screen of the laser light intensity transformation on the vertical transmission path of atmospheric turbulence. The phase screen simulation, low-frequency optimization, and scintillation index calculation methods are provided in detail, respectively. Based on the phase distribution of the laser beam, the scintillation index is obtained. Through the relationship between the scintillation index and the atmospheric turbulent refractive index structure constant, the atmospheric turbulence profile is inverted. The simulation results show that the atmospheric refractive index structure constant profile obtained by the iterative method is consistent with the input HV5/7 model below 6500 m, which has great guiding significance to carry out actual experiments to measure atmospheric turbulence using the Mie lidar.