Free-space quantum key distribution (QKD) system is one of the key parts of global quantum secure communications. So it is important to analyze the effect of turbulent atmosphere channel on quantum key distribution systems. The effect of turbulent atmosphere channel on quantum bit error rate (QBER) of a free-space QKD system based on BB84 protocol is described quantatively by near-field beam propagation theory and statistical method. The results indicate that, when the atmospheric attenuation coefficient is below -3 dB/km, it has a severe influence on the QBER of a free-space QKD system; and that in the area where atmospheric propagation factor coefficient is less than 0.5, QBER of system is ten times of that of the system operating without turbulence.