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Metal–organic frameworks (MOFs), a new type of porous functional material, have attracted widespread attention in the field of adsorption separation, medicine, and catalysis, etc., due to their unique adjustable pore structure and large specific surface. The defective zirconium-based MOF is rich in terminal Zr–OH induced by the lack of linkers and the μ3-OH originating from the Zr cluster, exhibiting high affinity for the carboxyl and sulfonic acid groups in the dyes. We report the performance of two defective zirconium-based MOFs (MOF-808 and MIL-140C) to remove Eosin y (EY), Methyl orange (MO), and Orange g from the water. Owing to the strong affinity, larger specific surface area, and better-matched pore structure, MOF-808 exhibits higher adsorption capacity for EY and MO, with maximum adsorption capacities of 661.7 mg g−1 and 532.4 mg g−1, respectively. The adsorption kinetics, thermodynamics, adsorption cycle performance, and adsorption mechanism of two MOFs for three dyes were investigated. Adsorption thermodynamics and XPS analysis certified that both chemical adsorption and physical adsorption occur during the adsorption process, especially chemical adsorption. Desorption and regeneration tests demonstrate that both MOF-808 and MIL-140C maintained their high adsorption capacity after four cycles, indicating two MOFs are favorable candidates for removing pollutants. In this article, the adsorption performance of MOF-808 and MIL-140C on three different sizes and structures of anionic dyes is mainly studied. The results show that MOF-808 has better adsorption performance for EY and MO. At the same time, the adsorption results show that the chemical adsorption between the adsorbate and the MOFs material plays a leading role in the adsorption, resulting in a high adsorption capacity for EY, although the EY molecule has a larger molecular size. [ABSTRACT FROM AUTHOR]