The invention relates a three-dimensional full waveform inversion energy weighted gradient preprocessing method. The method comprises the steps of (1) carrying out time second-order space finite difference method 3D forward simulation, storing a boundary wave field, and storing the maximum amplitude of reaching each speed grid point at the same time, (2) carrying out source wavefield reconstruction and residual wave field backward spreading at the same time, and carrying out corresponding time correlation to obtain a gradient, (3) reading the information stored in the step (1) and obtaining an energy weighted operator to carry out preprocessing of the gradient, and (4) obtaining the gradient operator of an appropriate step length action after preprocessing, and obtaining speed update quantity iterative update speed. According to the method, in the premise of not increasing computing amount, the problem of gradient operator deep and shallow layer energy imbalance caused by spherical wave spreading geometric diffusion and the like is solved, and the precision of deep layer speed imaging by full waveform inversion is improved effectively.