Four novel 3D metal–organic frameworks, [Ba (H₂O)₄ (L1)₂]·4H₂O (1), [Ba(H₂O)₄(L2)₂]·8H₂O (2) [Ba(H₂O)₇](L3)₂·2H₂O (3) and [Ba(H₂O)₇(L4)₂]·3H₂O (4) were obtained by self-assembly of barium(II) with four isoflavonesulfonate ligands [L1 = 7,4′-dihydroxyisoflavone-3′-sulfonate, L2 = 4′- hydroxy-7-methoxyisoflavone-3′-sulfonate, L3 = 5-hydroxy-7,4′-dimethoxyisoflavone-3′-sulfonate, L4 = 5,7-dihydroxy-6,4′-dimethoxyisoflavone-3′-sulfonate]. To survey the influences of different substituents in isoflavonesulfonate ligands on their self-assembly manners, the crystal structures of 1–4 have been determined by single-crystal X-ray diffraction. The results show that they have an intriguing variety of coordination modes and stacking manners with the changes of substituents in isoflavonesulfonate ligands. The sulfo-groups of isoflavonesulfonate ligands play important roles, they not only can coordinate with Ba²⁺ directly, but also provide an important bridge in a structural link between the hydrophilic region and the hydrophobic region in the crystal structure of 1–4.