Abstract: The refractive index structure constant is estimated and compared with measured values from micro-thermometer by using the meteorological parameters of Chengdu and Maoming, such as temperature, humidity and wind speed on two altitudes. The estimated model adopts MARIAH algorithm, which is based on the Monin-Obukhov similarity theory. The result shows that it is feasible to calculate the structure parameter by MARIAH algorithm. The trend and order of magnitude of the estimated structure constant fit well to that of the measured data. The correlation coefficients between estimated and measured values of two places are 0.86 and 0.92 while the mean absolute error values are 0.410 and 0.414 respectively. Besides, the estimated structure constant of Maoming is one order of magnitude larger than that of Chengdu.