The structures of multiply quantized vortices (MQVs) of equal-population atomic Fermi superfluid in a rotating spherical bubble trap are analyzed by solving the Bogoliubov-de Gennes (BdG) equation throughout the BCS-Bose Einstein condensation (BEC) crossover. Consistent with the Poincare-Hopf theorem, a pair of vortices emerge at the poles of the rotation axis in the presence of azimuthal symmetry, and the compact geometry provides confinement for the MQVs. While the single-vorticity vortex structure is similar to that in a planar geometry, higher-vorticity vortices exhibit interesting phenomena at the vortex center, such as a density peak due to accumulation of normal Fermi gas and reversed circulation of current due to in-gap states carrying angular momentum, in the BCS regime but not the BEC regime because of the subtle relations between the order parameter and density. The energy spectrum shows the number of the in-gap state branches corresponds to the vorticity of a vortex, and an explanation based on topological correspondence is provided.