The bit error rate（BER）of the laser communication system is brought by the atmospheric scintillation.The BER formula of the laser communication system at weak turbulence is deduced based on the statistical characteristic of the laser intensity variance and communication theory.The BER model of the laser communication system on the earth and from earth to space are established separately.The effect of the atmospheric turbulence,modulation,channel distance,laser wavelength and elevation on the BER is analysed by simulating the BER model.The changing law of the BER is discussed.It shows that the BER can be decreased by choosing appropriate modulation,laser wavelength,station position and elevation.