A spherical shearlet-based compression and reconstruction method for three-dimensional scalar information is disclosed. The method is used for processing data distributed in accordance to certain probability distribution in a three-dimensional space, and is especially suitable for processing random or deterministic scalar data having a spherical distribution feature under polar coordinates and being anisotropic on a sphere, including spatial data with physical significance and clinical observation data in biomedicine. In the present disclosure, on the basis of reasonably dividing the three-dimensional space into multiple concentric spherical layers, the three-dimensional data distribution is decomposed into multiple layers of spherical data. In each layer related spherical information is decomposed, and key information is extracted, compressed and stored by using the mathematical property of a spherical shearlet system, and the original three-dimensional data information can be reconstructed or approximately restored from extracted key data.