Abstract: In this paper, the relation between anti-interferences performances of Transform Domain Communication System(TDCS) and basis functions relational parameters are analyzed theoretically; a method of interferences mitigation one by one based on RAT+FRFT+IFRFT is proposed, it can avoid masking affection of strong jammer on weak jammer，and estimate the circumstance jams exactly; a method of system basis function generation based on sub-basis functions concatenation is proposed, these sub-basis functions are generated by the results of every jam estimation exactly and they are orthogonal with every corresponding jam, the circumstance jams spectrums are mitigated completely from system basis function with the method. The advantage anti-interferences performance and adaptability to communication circumstances for TDCS can be produced with the proposed methods.