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.