Compared with the traditional radio frequency link, free space optical communications (FSOC) system is a powerful supplement to existing wireless communications technology. In order to suppress the phase noise and intensity fluctuation of signal beam caused by atmospheric turbulence, it is necessary to monitor the condition of channel link in real time. Firstly, the measurement method of atmospheric refractive index structure constant based on spot centroid drift is introduced. All-day real-time monitoring of atmospheric refractive index structure constant is realized by using large aperture receiving target and narrow band filter combined with real-time image processing algorithm. Refractive index structure constant and intensity scintillation index are compared and analyzed. The measurement results show that there is a good linear relationship between their envelopes, which further verifies the reliability of our real-time measurement system.