The determination of the light spot center of mass is a key step in the refraction based measurement of atmospheric temperature gradient. An algorithm for the calculation of the light spot image’s center of mass is introduced. The calculation is used in the refraction based atmospheric temperature gradient measurement. An adaptive auto thresholding method is used in the algorithm which is suitable for various ambient environments. Experiment shows that the algorithm can be implemented easily and run in real-time; it is suitable to be used in the atmospheric temperature gradient measurement.