The invention discloses a mixed domain seismic migration Hessian matrix estimation method, and relates to the technical field of exploration geophysics, and the method comprises the steps: firstly obtaining an initial imaging result through employing a conventional migration method, then taking the migration result as a reflectivity model, carrying out the linear forward modeling and migration, and obtaining a secondary imaging result, using the two offset results for estimating an unstable phase filter in a space-wavenumber domain for approximating a Hansen matrix, calculating the inverse of the Hansen matrix by using mixed domain deconvolution, and using the estimated inverse of the Hansen matrix as a functional gradient in least square offset to improve the convergence rate of inversion, so that the inversion accuracy is improved. And the least square inversion is converged to an accurate solution within 4-5 iterations. The method has the advantages that the method is high in calculation efficiency, the least square migration convergence speed can be increased, the calculation cost of least square reflectivity inversion is reduced, and the method has good application prospects.