On the basis of the experimental methods of flocculated decolorization and equilibrium dialysis, the effect of dye structure on the interaction between organic flocculant PAN-DCD and dye has been explored. It was found that, under acidic conditions, PAN-DCD is effective in the decolorization of dyes with sulfonic acid groups and carboxyl groups and that the number of these groups has something to do with decolorization effectiveness. The more acidic groups in the dye, the greater the interaction extent between the flocculant and the dye and the higher the decolorization efficiency (DE) of the dye. Meanwhile, the hydrophobic groups in dyes also affect the binding of the dyes by PAN-DCD. The more hydrophobic groups in the dye, the higher the DE of the dye. The bigger the hydrophobic group in the dye, the more intensive the interaction of the dye with the floculant. Furthermore, amino and hydroxyl groups in dyes are related to the DE of the dyes as well, according to the formation of a hydrogen bond with the groups in the macromolecule. Therefore, the process of flocculated decolorization, resulting from the interaction between dye molecules and the flocculant, is controlled by both energetic and hydrophobic interactions.