Organic dye pollutants in wastewater have always been one of the most serious environmental problems. Most of the chromogenic groups in organic dye, especially for cationic molecules, are nitrogenous groups, and their reduction is easy to form toxic amines. Realizing the special removal of these contaminants from wastewater is of great significance nowadays. β-Cyclodextrin (β-CD) as an environmentally friendly and inexpensive supramolecular host compound is usually used for selectively encapsulating various molecules through the supramolecular inclusion. Herein the supramolecular inclusion technology for the removal of cationic organic dye pollutants in wastewater was proposed using a novel water-insoluble β-CD derivative as a case study. Five alkoxydifluoro-p-phthalonitrile substituted β-CDs (Rx-β-CDs) were synthesized through the two-step aromatic nucleophilic substitution reaction. The structural characterizations indicate that these water-insoluble Rx-β-CDs are mono-substituted products with a small surface area of less than 10 m2 g−1. The removal performances of Rx-β-CD for cationic, anionic and electrically neutral organic dye pollutants were approached systematically. It was found that Rx-β-CD was highly efficient for removing the cationic pollutants. The removal of cationic methylene blue was very fast and could reach equilibrium of close to 100% within 1–3 min. The removal mechanism was confirmed that the special removal of cationic organic dye pollutants by Rx-β-CD is a supramolecular inclusion process. This study sets up a new method for selectively removing cationic organic contaminants from wastewater.