The invention discloses an iteration frequency domain minimum mean square error equilibrium method under a double-dispersion channel based on weighted score Fourier transformation, and relates to an iteration frequency domain minimum mean square error channel equilibrium method in a mixed carrier wave communication system under a wireless double-dispersion channel or an underwater acoustic susceptance channel, in order to solve the problem of energy dispersion of signals on a time domain or a frequency domain at the same time. The method comprises the following steps that: firstly, a mixed carrier wave modulation system emitting end completes the mixed carrier wave modulation; secondly, a cyclic prefix is added for a time domain sequence x and is subjected to parallel-serial conversion; thirdly, a time domain sampling sequence is transmitted in serial; fourthly, the mixed carrier wave modulation system receiving end neglects a CP (computer program) part; fifthly, the time domain sampling sequence y is subjected to DFT (discrete Fourier transformation) at N points; sixthly, sampling points at the frequency corresponding to a certain sub carrier wave of the frequency domain are subjected to linear MMSE (minimum mean square error) estimation and N-point-stage WFRFT (weighted score Fourier transformation); seventhly, apriori information and Rho s=X(s, s) are estimated gradually; eighthly, the apriori information of the corresponding frequency domain is calculated; ninthly, the apriori information is fed back. The iteration frequency domain minimum mean square error equilibrium method under the double-dispersion channel based on weighted score Fourier transformation provided by the invention is applied to the mobile communication field.