Aimed at the problem that it is difficult for FRFT-TDCS to get rid of multi-component LFM interference signals by the traditional TDCS threshold design methods, this paper proposes a threshold design method based on noise estimation for FRFT-TDCS. On the basis of analyzing the FRFT domain spectrum distribution characteristics of LFM interference signals and noise, the paper obtains a set of unoccupied spectrum subcarrier through the FRFT domain energy broadening and position of interference signals, and determines the system adaptable threshold according to the amplitude statistical properties of Gaussian white noise and the requirements of system performance. The simulation results show that the proposed method can eliminate the single component LFM interference signal spectrum while λ>2.6, can eliminate the multicomponent LFM interference signal spectrum, and can retain “clean” spectrum while 3<λ<2.2. Compared with the traditional hard threshold setting method, the proposed method can achieve a better effect of interference eliminating and performance of BER under condition of multi-component LFM interference signals .