In the current context of environmental degradation, the development of novel size- and ion-selective adsorption materials for efficient wastewater treatment is a pressing concern. In this study, the selective adsorption properties of the metal–organic frameworks UiO-66, sulfo-functionalized UiO-66, and amino-functionalized UiO-66 are investigated using the organic dyes methylene blue, rhodamine B, methyl orange, and acid red 52 as model pollutants. Owing to the different molecular size of the dyes, UiO-66 showed a high adsorption capacity for methylene blue and methyl orange, whereas large rhodamine B and acid red 52 were not easy to be adsorbed in the micropores of the UiO-66 framework. In addition, the sulfo- and amino-functionalization of the UiO-66 framework enhanced the adsorption capacity for methylene blue and methyl orange, respectively. The ion-selective adsorption properties of the UiO-66 framework were demonstrated using mixed solutions of methylene blue and methyl orange. Although both compounds were moderately adsorbed into UiO-66, methylene blue and methyl orange were selectively adsorbed using sulfo-functionalized UiO-66 and amino-functionalized UiO-66, respectively. This combined size-selectivity and ion-selectivity renders functionalized UiO-66 a promising adsorbent for the removal of organic pollutants from aqueous solutions.