Aiming at the problem of accurate estimation of coherent parameters for the distributed coherent jamming system (DCJS), this paper first establishes a transmit-receive signal model of the DCJS in the presence of coherent parameter estimation errors. Then, it analyzes and verifies that the generalized cross-correlation function weighting method causes a decrease in the estimation accuracy of coherent parameters due to whitening processing, which in turn impairs the synthesis efficiency of the DCJS. Finally, a coherent parameter estimation method based on frequency-domain feature matching is proposed. The weighting method based on frequency-domain feature matching can effectively preserve the intra-pulse features of signals, thereby improving the estimation accuracy of coherent parameters. Simulation results show that, compared with the existing algorithms, the proposed method improves the time delay estimation accuracy by 30% and the phase difference estimation accuracy by 7.7%.