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In order to research the influence of atmospheric turbulence on bit error rate of incoherent flat-topped Gaussian beam communication system, the equation of laser transmitting through atmospheric turbulence channel was analyzed, under the condition of ignoring other noises in the system, but considering the noises caused by atmospheric turbulence only. The relationship between the BER induced by scintillation and propagation distance was obtained for different wavelengths with different modulation. Similarly, the relationship of BER and N, which presents the number of Gaussian sources added to form the flat-topped Gaussian beam, was obtained with different Gaussian source sizes for different wavelengths. The results show that the BER of atmospheric turbulence channel is smaller for beams with a higher order N and a larger Gaussian source size. With a higher order N, the BER for 0.85μm beam is lower than that of 1.55μm beam. For PSK modulation, the BER performance is better, and it can decrease the BER of laser communication link effectively.