The role of chiral counterions on the attraction and self-assembly of chiral Pd12L24 metal organic cages (MOCs) with NO3- being the original counterion is studied by laser light scattering and isothermal titration calorimetry. Nitrates can trigger the self-assembly of macrocationic Pd12L24 into hollow spherical blackberry-type supramolecular structures via counterion-mediated attraction. Although chiral counteranions, such as N-(tert-butoxycarbonyl)-alanine (Boc-Ala), have weaker interaction with the MOCs compared to NO3-, they can induce different assembly behaviors between two enantiomeric MOCs by inhibiting the MOC-nitrate binding and weakening the interaction between them. The D-counterions are capable of selectively suppressing and slowing down the assembly of L-MOCs and also considerably decreasing their assembly size due to the much weaker MOC-nitrate interaction. The same scenario is observed for L-counterions when interacting with the D-MOCs. This study unveils the role of weakly associated chiral counterions on the central chiral macroions, especially their supramolecular structure formation, and provides additional evidence on the mechanism of the homochirality phenomenon.