AbstractHerein the defect engineering is reported in zirconium 1,4‐dicarboxybenzene metal‐organic frameworks (UiO‐66) both inducing new adsorption sites and enhancing the adsorption affinity of indole adsorbates. The result shows that high adsorption energies for indole are obtained at the deprotonated μ₃‐O, followed by unsaturated Zr‐cation sites in defective UiO‐66 structures. The key interactions are the hydrogen bonding between the hydrogen donor NH group of indole with the negative charge oxygen atom of the induced μ₃‐O site and the dative covalent bond between the nitrogen atom of indole with the unsaturated Zr‐cation. For hydrogen bonding, the binding energies tend to increase with the increasing of defect concentrations and spread a broad range up to ≈−2.00 eV. It is also shown that the vibrational modes of indole molecules are influenced by their adsorption sites. Accordingly, the NH stretching modes of the adsorbed indole are redshifted ≈100–300 cm⁻¹ compared to its counterpart in the isolated indole. The strongest redshift is obtained for indole adsorbed at the μ₃‐O site with three missing linkers. The occupation of water at the active sites may enhance or diminish the adsorption affinity of indole relying on the hydrogen bonding mechanism.