The invention relates to a prestack geostatistical inversion method under three-dimensional double control. The method comprises the steps of (1) target work area petrophysical analysis and well seismic calibration, (2) the construction of a low-frequency model under seismic velocity constraints, (3) prestack simultaneous inversion based on partial superimposed seismic data, (4) lithologic fluid probability analysis, and (5) geostatistical inversion under three-dimensional double control constraints. According to the method, in the calculation of a parameter of geostatistical inversion prior information lithology probability, firstly, the deterministic inversion is carried out, based on the Bayesian discriminant principle, elastic data obtained by inversion is converted into a three-dimensional lithological probability body, the three-dimensional lithological probability body is taken as prior information to replace traditional zero-dimensional lithologic probability constrained geostatistical inversion, the frequency merging and frequency-down processing are carried out on a final inversion result, therefore, while the longitudinal resolution of the geostatistical inversion is improved, original seismic structure characteristics still can be maintained, the inversion uncertainty is reduced, and the invention still has good predictive ability.