Based on the virtual temperature, wind speed and H2O concentration data respectively measured by the sonic anemometer and Li7500 CO2/H2O analyzer sensor in the summer of Hefei, the effects of humidity fluctuation on the measurement of the refractive index structure parameter C2n for visible radiation by sonic anemometer from two aspects are studied. The real temperature from virtual temperature via humidity corrections is obtained. Temperature structure parameter C2T respectively calculated via real temperature and virtual temperature is compared. In the other side, the contributions of humidity structure parameter C2q and temperature-humidity correction CTq on C2n are calculated. The results show that the distinction between C2T calculated via real temperature and virtual temperature is obvious, and the difference is more than 10% most of the time. The contribution of CTq can be more than 10%, and it can′t be ignored. The contribution of C2q is extraordinarily small, lower than 5%, and it can be ignored.