IRMOF-3 and its modifications, known as IRMOF-3−MWCNT-OH and IRMOF-3−MWCNT-OH−Pd-NPs, are prepared and characterized using Fourier transform infrared spectroscopy, infrared spectroscopy, field emission scanning electron microscopy, X-ray diffraction, energy dispersive spectroscopy, and Brunauer− Emmett−Teller (BET) analysis. These adsorbents, especially IRMOF-3−MWCNT-OH−Pd-NPs, are proposed as a novel adsorbent to remove malachite green (MG) dye from aqueous solutions. In this way, several parameters including initial dye concentration, pH, adsorbent mass, and sonication time are considered as the effective parameters that must be optimized. Using the optimized parameters obtained by the central composite design approach for the IRMOF-3, IRMOF-3−MWCNT-OH, and IRMOF-3−MWCNT-OH−Pd-NPs leads to maximum adsorption efficiencies of 37.20%, 55.50%, and 96.10%, respectively, while under the same conditions, the removal percentage significantly increases when the adsorbent is modified with MWCNT-OH and Pd-NPs. For instance, at 4 mg L −1 MG concentration, 5.5 for pH value, 12.5 min sonication time, and 0.01 g of adsorbent mass, an adsorption efficiency of 21.10%, 35.00%, and 96.80% is obtained, respectively. In addition, zero point charge analysis performed for IRMOF-3, IRMOF-3−MWCNT-OH, and IRMOF-3−MWCNT-OH−Pd-NPs demonstrates quantitative values of 3.30, 3.50, and 3.80, respectively. Besides, isotherms, kinetics, and thermodynamics investigations revealed that a pseudo-first-order, Langmuir isotherm model and endothermic reaction introduce the best modeling behaviors for MG adsorption onto the three aforementioned adsorbents. Moreover, the measured BET surface area reveals that the BET for IRMOF-3, IRMOF-3−MWCNT-OH, and IRMOF-3−MWCNT-OH−Pd-NPs before and after adsorptions are 52.03 and 41.39 m 2 g −1 , 207.51 and 205.18 m 2 g −1 , and 194.96 and 31.78 m 2 g −1 , respectively. Finally, reusability analysis results reveal that among the examined adsorbents, IRMOF-3 introduces no reusability potential, while IRMOF-3−MWCNT-OH and IRMOF-3−MWCNT-OH−Pd-NPs have three and five sequential recoveries, respectively.