A pyridine/aniline appended unsymmetrical bidentate ligand N-(4-(4-aminobenzyl)phenyl)nicotinamide, investigated in this work has two well-separated coordination sites. Combination of the ligand with cis-protected palladium(II) (i.e., PdL′) and palladium(II) in separate reactions produced the corresponding Pd2L′2Lun2 and extremely rare Pd2Lun4 type self-assembled binuclear complexes, respectively. Notably, both varieties of complexes are prepared from a common ligand system. Two diastereomers (i.e., (2,0) and (1,1)-forms) are possible for Pd2L′2Lun2 type complex, whereas four diastereomers (i.e., (4,0), (3,1), trans(2,2), and cis(2,2)-forms) can be imagined for the Pd2Lun4 type complex. However, exclusive diastereoselectivity was observed, and the complexes formed belong to (1,1)-Pd2L′2Lun2 and cis(2,2)-Pd2Lun4 forms. The diastereomers are predicted from NMR study in solution and DFT calculations in gas-phase and implicit-solvent media; however, single-crystal structures of both the complexes provided unambiguous support. The rare Pd2Lun4 type complex is studied in further detail. Parameters like counteranion, concentration, temperature, and stoichiometry of metal to ligand did not influence the diastereoselectivity in complex formation. DFT calculations show the cis(2,2) form to be the most stable, followed by the (3,1) isomer. The lowest conformational strain in the bound ligand strands in the cis(2,2)-arrangement along with optimal intermolecular interactions makes it the energetically most stable of all the isomers. Molecular dynamics (MD) simulations were carried out to visualize the self-assembly process toward the formation of Pd2Lun4 type complex and the free energy difference between the cis(2,2) and (3,1) isomers. Snapshots of MD simulation elucidate the step-by-step progress of complexation leading to the cis(2,2)-isomer. Copyright © 2020 American Chemical Society.