Understanding the character of superatom molecular orbitals (SAMOs) of fullerenes, especially those of the endohedral fullerenes, can potentially facilitate the utility of these molecules in organic electronics beyond conventional limits. However, the detailed nature of SAMOs in molecular films on substrates has yet to be unraveled. Using density functional theory, we investigate the wavefunction distributions and electronic structures of SAMO states of a Li@C60 monolayer in dependence on the position of Li within the cage and the type of substrate species. We find that the characteristics of the SAMOs in terms of shape and energy are quite sensitive to the Li position due to different charge redistributions. The substrate affects the intermolecular distances in the Li@C60 films and modifies the widths and dispersion of the SAMO bands while retaining energetics similar to that of the isolated Li@C60 monolayer. The substrate also affects the SAMO effective masses, making it possible to tune them via substrate-induced interaction. A properly chosen substrate can so be beneficial for Li confinement and SAMO stability, reflecting the molecule–substrate interaction and the charge transfer at the interface. These findings provide insights into the design and engineering of SAMOs of molecular films.