Atmospheric turbulence has a great influence on the performance of the atmospheric laser communication system reducing the signal to noise ratio (SNR) and increasing the bit error rate (BER). However, there is rarely study on the effect of atmospheric turbulence on the power spectrum of the rectangular pulse. In this paper, a spectral analyzing method is used to analyze the influence of atmospheric turbulence on the signal. An experiment of laser beam propagation characteristic is carried out on a 6km horizontal atmospheric link, the wavelength is 808 nm. The signal is 100MHz rectangular pulse. The waveform of the rectangular pulse is collected by the oscilloscope, and the power spectral density of the signal is calculated and analyzed by the method of periodogram. Experimental results show that the response and noise characteristics of the laser and photoelectric detector have a great influence on the signal power spectrum distribution which can increase the noise component in the 10^6 Hz frequency range. After the atmospheric turbulence propagation, the signal power decreases in the whole frequency range. However, as the existence of atmospheric turbulence, the signal power increases in the atmospheric turbulence characteristic frequency (tens to hundreds of Hz). The noise power increases in the high frequency range (10^7~10^8 Hz).