Fluoride ion (F−) is one of the most hazardous elements in potable water. Over intake of F− can give rise to dental fluorosis, kidney failure, or DNA damage. As a result, developing affordable, equipment-free and credible approaches for F− detection is an important task. In this work, a new three dimensional rare earth cluster-based metal-organic framework assembled from lanthanide Y(III) ion, and a linear multifunctional ligand 3-nitro-4,4′-biphenyldicarboxylic acid, formulated as {[Y(μ3-OH)]4[Y(μ3-OH)(μ2-H2O)0.25(H2O)0.5]4[μ4-nba]8}n (1), where H2nba = 3-nitro-4,4′-biphenyldicarboxylic acid, has been hydrothermally synthesized and characterized through infrared spectroscopy (IR), elemental and thermal analysis (EA), power X-ray diffraction (PXRD), and single-crystal X-ray diffraction (SCXRD) analyses. X-ray diffraction structural analysis revealed that 1 crystallizes in tetragonal system with P4¯21m space group, and features a 3D framework with 1D square 18.07(3)2 Å2 channels running along the [0,0,1] or c-axis direction. The structure of 1 is built up of unusual eight-membered rings formed by two types of {Y4O4} clusters connected to each other via 12 μ4-nba2− and 4 μ3-OH− ligands. Three crystallographic independent Y3+ ions display two coordinated configurations with a seven-coordinated distorted monocapped trigonal-prism (YO7) and an eight-coordinated approximately bicapped trigonal-prism (YO8). 1 is further stabilized through O-H⋯O, O-H⋯N, C-H⋯O, and π⋯π interactions. Topologically, MOF 1 can be simplified as a 12-connected 2-nodal Au4Ho topology with a Schläfli symbol {420·628·818}{43}4 or a 6-connected uninodal pcu topology with a Schläfli symbol {412·63}. The fluorescent sensing application of 1 was investigated to cations and anions in H2O. 1 exhibits good luminescence probing turn-on recognition ability toward F− and with a limit detection concentration of F− down to 14.2 μM in aqueous solution (Kec = 11403 M−1, R2 = 0.99289, σ = 0.0539). The findings here provide a feasible detection platform of LnMOFs for highly sensitive discrimination of F− in aqueous media.