Nine new coordination polymers: [Cu3(ipO)2(pyz)2] (5), [Cu3(ipO)2(4-phpy)(H2O)2] (6), [Cu(ip)(4-phpy)2] (7), [Cu3(ipO)2(H2O)2] (8), [Co(phen)(ip)(H2O)] (9), [Co3(1,2,3-btc)2(4,4′-bpy)2(H2O)2]·2H2O (10), [Ni(1,2,3-btcH)(4,4′-bpy)(H2O)]·H2O (11), [Cd5(1,2,3-btc)2(1,2,3-btcH)2(4,4′-bpy)3(H2O)2] (12) and (1,2,3-btcH3)(4,4′-bpy) (13) (1,2,3-btcH3 = 1,2,3-benzenetricarboxylic acid, ipO = 2-hydroxyisophthalate, 4,4′-bpy = 4,4′-bipyridine, pyz = pyrazine, 4-phpy = 4-phenyl-pyridine and phen = o-phenanthroline) have been hydrothermally synthesized. This family of compounds show the role of the N-containing heterocyclic ligands and Cu(II) ions in the metal–ligand reactions. These results suggest that the hydroxylation requires Cu(II) ions as the oxidant, rather than the presence of N-containing heterocyclic ligands, while the decarboxylate procedure requires high temperature and basic condition rather than the participation of Cu(II) ions. The obtained compounds show versatile structures and magnetic properties due to the flexibility of the carboxylate ligands. Compound 5 shows dominated antiferromagnetic interaction in the [Cu2(μ-ipO)2] unit, and no long-range magnetic ordering behaviour. Compound 10 has a topologically ferrimagnetic chain with alternating CoIIoctCoIItetCoIIoct (oct = octahedral, tet = tetrahedal) spin arrangement. The CoIItet and CoIIoct ions are bridged by similar syn–anti carboxylates (CoIItet⋯CoIIoct 4.616 and 4.735 Å). Such a chain shows ferro- and antiferro- magnetic interactions and no long-range magnetic ordering behaviour was observed. Compound 11 has a antiferromagnetic coupled syn–anticarbxylate-bridged Ni(II) chain (J = 1.48(2) K), and shows long-range magnetic order below 2.6 K due to the extensive hydrogen bonds between the chains.