A novel metal–organic framework, [(CH₃)₂NH₂]₂[Cu₃O(SO₄)₃Cu₂L₂(DMF)(H₂O)]·9DMF (JLU-Liu39) H₂L = pyridine-3,5-bis(phenyl-4-carboxylic acid), has been successfully synthesized under solvothermal conditions. Structure analysis indicates that the framework of JLU-Liu39 is constructed by ternary building units which include a rare hexa-nuclear [Cu₆O₂(SO₄)₆] cluster, a classical [Cu₂(CO₂)₄] paddlewheel, and a 3-connected hetero-N, O donor ligand. The whole 3D framework possesses a (3,4,4)-connected fjh topology and a large window size of 25.3 Å with high solvent-accessible volume accounting for approximately 75.8% of the cell volume. On the basis of the anionic framework and large pore volume, JLU-Liu39 can efficiently adsorb cationic dyes such as MLB, MV, RhB and neutral dye NR but exclude anionic dyes such as MO and Orange II. Moreover, JLU-Liu39 also exhibits size-exclusion performance for dyes of different sizes, and the dye adsorption amounts decrease with the increase of dye size. With respect to the proportional mixture dyes with different charges for MO & MLB and Orange II & MLB, JLU-Liu39 can be able to selectively adsorb the cationic dye MLB efficiently. Based on the aforementioned considerations, JLU-Liu39 is a good anionic-skeleton MOF material for the adsorption and separation of organic dyes.