With the excellent ability of anti-jamming, the traditional transform domain communication system (TDCS) is limited in wide application due to the same electromagnetic environment between the transmitter and the receiver. Based on the traditional TDCS, a long-distance aviation transform domain communication system (LDA-TDCS) is presented to realize the aviation communication under complex electromagnetic environment. The scheme and function model of LDA-TDCS are introduced, and its every function module is analyzed in detail. Since the basis functions are transmitted reliably with M-ary spread spectrum technique, the LDA-TDCS is converted to the equivalent traditional TDCS. The simulation results by MATLAB show that the anti-jamming performance of LDA-TDCS is better than that of DSSS (direct spread spectrum system) under multiple tones jamming.