The refractive index fluctuation of atmosphere are mainly caused by variations in temperature and humidity. A new method of studying effects of humidity fluctuation on the structure parameter of the refractive index is proposed. Humidity fluctuations is obtained from fluctuations of ‘sonic temperature’, very closely equivalent to virtual temperature ,using a three-component sonic anemometer. The structure parameters C2Q, CTQ, can be calculated. C2n and temperature fluctuation, humidity fluctuation are measured by a sonic anemometer and microthermal probe both in dry desert and in damp sea shore. Meanwhile, the humidity fluctuation can be estimated by a mode using field experiment meteorologic condition as input parementers. Both measurement and mode show that humidity directly influencing C2n can be ignored. Humidity effects is mainly achiered associating with temperatime fluctuation. Generally, the contribution to C2n is less than 10% except near a marine surface or saturated soil especially during occurrence minimal C2n before sunset.