In this work, a simple metal-organic framework (MOF) material, UiO-66-NH₂, was prepared for the highly efficient separation of artemisinin (Art) and artesunate (Aru). Selective adsorption tests showed that UiO-66-NH₂ presented a much higher selectivity toward Aru than Art (α_Aru/Art = 40.74). The N₂ adsorption-desorption isotherm results of UiO-66-NH2 indicated a suitable pore size to enable the free entry of Art and Aru. Contact angle analysis indicated that UiO-66-NH₂ is hydrophilic with the -NH₂ group, and can interact with the hydrophobic Aru through hydrogen bonding between the -NH₂ and -COOH groups, which is not possible with the hydrophobic Art. The selective adsorption of Aru onto UiO-66-NH₂ may be attributed to three factors: pore size, functional groups, and difference in hydrophobic/hydrophilic characteristics between the adsorbent and adsorbate. Molecularly imprinted polymers (MIPs) were prepared using Aru as a template for selective adsorption experiments to verify the excellent selectivity of UiO-66-NH₂. The adsorption amount (65.24 mg g⁻¹) and selectivity factor (α_Aru/Art = 40.74) of UiO-66-NH₂ toward Aru were significantly better than those of the MIPs (2.039 mg g⁻¹ and 3.072, respectively). The binding capacity and better selectivity of UiO-66-NH₂ provide evidence supporting the potential of MOF adsorbents for the separation of various analogous molecules.