Based on the finite element method of structural mechanics, the two-dimensional stacking structure of soft spherical shells under gravity is studied by using the area of soft spheres and the distribution of the number of adjacent spheres, and the filling rate and potential energy of the stacking structure are analyzed. The results show that the soft spherical shell stacking process is disordered and has no orientation preference. There are different types of stacking structures, and different types correspond to different areas and distributions of adjacent spheres, which exhibit polydispersity characteristics. The area change rate of the stacking structure is positively correlated with the potential energy of the stacking structure. The greater the area change rate results the greater the potential energy, and the potential energy of the structure type decreases with the increase of the modulus. For the stacking structures of bidisperse soft spheres with different radii, there is an approximate linear relationship between the area of the soft spheres and the number of adjacent spheres, and the more number of soft spheres with bigger radii in the structure results in the greater potential energy of the structure. This study helps to improve the understanding of the geometric and topological properties of soft matter packing structures such as cells, and provides a computational basis for the analysis of living tissues and materials with soft spherical shells.