Two 3D/2D anionic metal-organic frameworks (MOFs), [Cu(HL)]n (1) and [Mn3(L)2(DMF)4]n (2) (DMF = N,N-dimethylformamide), were synthesized by the solvothermal reaction of metal salts and 5'-(4-carboxyphenyl)-2',4',6'-triethyl-[1,1':3',1″-terphenyl]-4,4″-dicarboxylic acid (H3L). Single-crystal X-ray diffraction analyses revealed that complex 1 shows three-dimensional (3D) frameworks with a (3,6)-connected 3-fold interpenetrated topology with the Schläfli symbols of {4.62}2{42.610.83}, whereas the topology of the two-dimensional (2D) architecture can be defined as 2-fold stacked layers with the Schläfli symbols of {43}2{46.66.83} for complex 2. In addition, density functional theory calculations, together with UV-vis adsorption spectroscopy, zeta potential, effective aperture size analysis, TEM, and SEM, were also performed to determine the accurate adsorption sites and significant differences in dye adsorption for complexes 1 and 2. Interestingly, UV-vis studies confirm that Mn-MOF displays remarkable adsorption efficiency for cationic rhodamine B, methylene blue, malachite green, and methyl green, and the removal rate reached 95.2, 95.0, 87.0, and 78.0%, respectively, while almost no adsorption capacity was detected for anionic cresol red and methyl orange. However, Cu-MOF failed to efficiently adsorb any selected dyes. Moreover, the magnetic properties were also investigated through experimental and theoretical calculations in detail, which revealed the weak and stronger antiferromagnetic interactions that occurred between Cu(II) and Mn(II) centers, respectively. Finally, this work provides the profound mechanisms for magnetism and dye adsorption.