In this study, metal-organic framework MIL-53(Al) was synthesized and studied to understand the different mechanisms between normal MIL-53(Al) and 2D metal-organic framework MIL-53(Al) for removing fluoride. Comparatively, the 2D MIL-53(Al) had two-dimensional linear morphology rather than block shape, indicating more expose adsorptive sites than normal MIL-53(Al). The batch adsorption experiments were applied to investigate the performance of 2D MIL-53(Al), including pH, adsorption kinetics, and thermodynamics. The 2D MIL-53(Al) (75.50 mg/g) showed better adsorption capacity than normal MIL-53(Al) (35.63 mg/g). The adsorption process of 2D MIL-53(Al) followed the pseudo-first-order model and Langmuir model. The adsorption mechanism of this material was further studied by using experimental characterization and density functional theory calculations in detail. The main adsorptive sites were Al and O in the 2D MIL-53(Al), and the relationship between fluoride binding with Al and O was HF₂^– > HF > F^–. The species of fluoride were HF₂^–, HF, F at different pH and concentrations. Hence, this study provides a significant way on the application of two-dimensional materials for removing fluoride.