The atmospheric transmittance is valuable in designing and applying free space optical communication system. The precision of classical method can not meet actual needs. In this paper, by ameliorating classical method of measuring atmospheric transmittance, and combining the Gauss distribution of the energy of the laser beam and the turbulent influence existing in the atmospheric channel, the experiment scheme of accurately measuring atmospheric transmittance is designed. Actual atmospheric transmittance of several free space channels in Shanghai and Qinghai are measured. The results of classical method and the method which we mention above are different. The results show that, in Qinghai, the transmittance is high, but turbulence is bad; in Shanghai, the situation is opposite. The analytic and experimental results also indicate that the distant turbulent channels influence facular spread strongly.