Sodium 4 '-methoxy-5,6,7-trihydroxyisoflavone-3 '-sulfonate (1) is synthesized by the sulfonation of 6-hydroxybiochanin A and its structure is characterized by elemental analysis, H-1-NMR, and IR spectroscopy. It is assembled with cobalt(II) or zinc(II), hexaquacobalt(II) bis(4 '-methoxy-5,6,7-trihydroxyisoflavone-3 '-sulfonate) tetrahydrate (2) and hexaquazinc(II) bis(4 '-methoxy-5,6,7-trihydroxyisoflavone-3 '-sulfonate) tetrahydrate (3) are obtained and characterized by IR spectroscopy. Simultaneously, their three-dimensional structures are determined by single-crystal X-ray analysis. It turns out that 2 and 3 are isomorphous and crystallize in the triclinic crystal system, space group P-1. Hydrophilic regions are defined by O-H center dot center dot center dot O hydrogen bonds involving the coordinated water molecules, the included water molecules, and sulfonate groups. Aromatic pi...pi stacking interactions assemble the isoflavone skeletons into columns and these columns formed hydrophobic regions. The sulfonate group is an important bridge as a structural link between the hydrophilic regions and the hydrophobic regions. Hydrogen bonds, pi...pi stacking interactions and the electrostatic interactions assemble 2 and 3 into three-dimensional network structures.