In this paper, a method of single carrier frequency domain pre-equalization suitable for air-ground communication system uplink is brought forward under the condition of frequency-selective Rayleigh slow fading channel. A model of pre-equalization system is designed on the basis of this method. In the model, the downlink pilot signal is compared with the local one to perform channel condition estimation on ground station, and then the pre-equalization of uplink signal is processed by utilizing the acquired channel condition information. Finally, the uplink signal equalization is conducted on airborne receiver. The signal processing procedures of the method are analyzed and the coefficient of the pre-equalization are obtained based on zero-forcing criterion and minimum mean square criterion. By comparing the BER performance of different equalization schemes, the simulation results show that the error-floor effects will arise when pre-equalization is implemented only on ground transmitter; whereas, when bit error rate is 10-5, a 2 to 3 dB gain in performance is expected by the equalization made again on airborne receiver after ground pre-equalization in comparison with the former single carrier frequency equalization method with a linear equalization structure.