In order to solve the problem of communication interference in Transform Domain Communication System (TDCS) under complex electromagnetic environment, a TDCS model based on store and forward mechanism was proposed. Based on the analysis of the electromagnetic spectrum environment, the spectrum sensing cases of transmitter and receiver were classified according to their respective perceptions. With the analysis of consistent spectrum conditions, the TDCS model for long distance aviation communication system was established based on store and forward modules in inconsistent spectrum conditions, and the specific communication schemes were designed, which can effectively improve the system performance. The simulation results show that the interference model and spectrum setting are reasonable, the performance of TDCS is close to the ideal bit error rate under the condition of the same spectrum. Under the condition of different frequency spectrum with more concentrated comb spectrum interference, the bit error rate is reduced by about 24.48%; moreover, with the increase of Signal-to-Noise Ratio (SNR), the performance improvement is more obvious, and the performance improvement is about 1dB under the same bit error rate.