Molecular recognition based on cationic water-soluble pillar[n]arenes shows considerable advantages in their application in biological and environmental systems, such as excellent anion-binding ability and antimicrobial properties. Unique complex models are discovered in this work where a cationic water-soluble pillar[6]arene binds with disodium 1,5-naphthalenedisulfonate and disodium 2,6-naphthalenedisulfonate at the ratio of 1 : 2, which is proven by results from nuclear magnetic resonance spectroscopy, isothermal titration calorimetry, fluorescence spectroscopy experiments and transmission electron microscopy.