A chiral endohedral Pd12Ala24 metal-organic cage (MOC) incorporating enantiomeric tert-butyloxycarbonylalanine (Boc-Ala) ligands is synthesized as a model system of a chiral macrocation containing internal chiral centers away from the surface of the MOC. The endohedral chiral geometry leads to the interaction between these chiral centers inside the MOCs far away from other chiral components such as chiral counterions in solution. The consequence is that the chiral recognition (two MOC enantiomers self-assemble individually in their mixed solution) and chiral discrimination (self-assembly favors one enantiomer over the other) previously observed in the self-assembly of MOCs carrying exohedral chiral centers become weaker or completely disappear in the current MOC solutions, demonstrating that the effective electrostatic interaction in a short range is critical for the chiral recognition behavior of macromolecules during their self-assembly. Different small chiral species in solution (e.g., arabinose, lactate, tartrate, and gamma-cyclodextrin) show various capabilities on the chiral recognition and discrimination of endohedral Pd12Ala24 MOCs during the self-assembly, based on the size and charge of these species.