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The reconstruction methods of marine gravity anomaly encrypted reference map are studied in this study, which can improve the accuracy of underwater gravity matching navigation. Firstly, the mean sea surface as the third dimension component was introduced into the semivariance function of the traditional Kriging two-dimensional (2-D) interpolation method for the first time. After that, a new mean sea surface three-dimensional (3-D) correction method was proposed in order to improve the spatial resolution of the marine gravity anomaly reference map and minimize the loss of accuracy. Secondly, encrypting the spatial resolution of the marine gravity anomaly reference map from <inline-formula> <tex-math notation="LaTeX">$4^\prime \times 4^\prime $ </tex-math></inline-formula>, <inline-formula> <tex-math notation="LaTeX">$3^\prime \times 3^\prime $ </tex-math></inline-formula> and <inline-formula> <tex-math notation="LaTeX">$2^\prime \times 2^\prime $ </tex-math></inline-formula> to <inline-formula> <tex-math notation="LaTeX">$1^\prime \times 1^\prime $ </tex-math></inline-formula> as an example, respectively, under the same conditions, the reconstruction accuracy of the new proposed method improved 62.25&#x0025;, 140.92&#x0025; and 104.93&#x0025;, respectively. Thus, compared with the traditional Kriging 2-D interpolation method, we verified that the new proposed method had better reconstruction accuracy. Thirdly, based on the proposed new method, the spatial resolution of the marine gravity anomaly reference map was firstly encrypted from <inline-formula> <tex-math notation="LaTeX">$1^\prime \times 1^\prime $ </tex-math></inline-formula> to <inline-formula> <tex-math notation="LaTeX">$0.25^\prime \times 0.25^\prime $ </tex-math></inline-formula>. After that, transforming the spatial resolution of <inline-formula> <tex-math notation="LaTeX">$0.25^\prime \times 0.25^\prime $ </tex-math></inline-formula> into <inline-formula> <tex-math notation="LaTeX">$1^\prime \times 1^\prime $ </tex-math></inline-formula>, compared with the original model data of <inline-formula> <tex-math notation="LaTeX">$1^\prime \times 1^\prime $ </tex-math></inline-formula>, its the final RMSE is <inline-formula> <tex-math notation="LaTeX">$4.143\times 10^{-1}$ </tex-math></inline-formula> mGal, which further verified the validity and reliability of the new mean sea surface 3-D correction method in application.