The self-assembly of Zn(II) and Cd(II) ions with two isomeric tetradentate ligands, 2-pyridyl-isonicotinoylhydrazone (HL1) and 2-benzoylpyridyl-picolinoylhydrazone (HL2), was studied by elemental analysis, FT-IR spectroscopy and single-crystal X-ray diffraction. The reaction of zinc(II) and cadmium(II) salts with HL1 and HL2 in methanol under solvothermal conditions produced six monomer and one tetranuclear zinc(II) complexes, namely, Zn(HL1)Br2 (1), Zn(HL1)Cl2 (2), [Cd(HL1)2](NO3)2·H2O (3), Cd(HL2)Br2(4), Zn(HL2)Cl2 (5), Zn(HL2)Br2 (6) and [Zn4(L2)4I2][ZnI4]·2H2O (7). The structure of 7 includes a cationic tetranuclear cluster of four zinc ions, four ligands, and two anions, counterbalanced by ZnI42− ions. However, the reaction of zinc(II) and cadmium(II) salts with HL1 under the same conditions produced monomer compounds. Herein, the ligand effects on the complex structures were studied. Hirshfeld surface analysis and fingerprint plots facilitate the comparison of intermolecular interactions in compounds 1–7, which are crucial in building supramolecular architectures.