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In this study, a facile strategy of regulated self-assembly synthesis of Mn-MIL-100, using sodium acetate (CH₃COONa) as a mono-dentate ligand capping agent (CA), was proposed. The as-prepared product is denoted Mn-MIL-100-CA. The coordination modulation of CH₃COONa, led by its interference in the connectivity and symmetry of the metal centers and organic nodes, plays a vital role in the synthesis process. The crystallinity, morphology, topology, and properties of such MOF products were improved, since the self-assembly process of Mn-MIL-100-CA was promoted and regulated effectively. The materials were systematically characterized via XRD, SEM, N₂ isotherms, XPS, and TGA in terms of crystallization behavior, morphology, topology, chemical composition, and thermal and water stability. The ability of Mn-MIL-100 and Mn-MIL-100-CA to remove methylene blue (MB) from an aqueous solution was investigated using a UV–vis spectrophotometer. The results indicate that with the addition of a molar ratio of 50% CH₃COONa, Mn-MIL-100-CA particles developed a regularly symmetrical morphology, i.e., ‘spherical pyramid-like structure’ crystals with a dimension of 2~5 μm. Their specific surface area and pore volume increased by 59.2% and 56.7%, respectively. The increased proportion of Mn³⁺ implies reduced crystal defects and improved crystal structural order and integrity, and therefore an enhanced water stability. Mn-MIL-100-CA exhibited excellent adsorption performance towards MB from aqueous solution. The equilibrium adsorption value was as high as 1079.9 mg/g, which is 44.7% higher than that of Mn-MIL-100 without the addition of CA. The good adsorption capacity and excellent water stability mean that Mn-MIL-100-CA has great potential for the practical removal of MB dye pollutants from water.