Zr-based metal-organic frameworks (Zr-MOFs) are emerging as potential adsorbents for removing nitrogen contaminants in fuel and wastewater. Functionalized Zr-MOFs exhibited superior indole (IND) adsorption capacity than the original MOF, but the activity of the multiple adsorption sites has not been discussed. Through experiment measurement and Density Functional Theory (DFT) calculations, this research investigated the IND adsorption mechanism at various sites on Zr-BDC-NH2 and Zr-BDC-NO2. Based on the adsorption isotherm, the adhesion of IND with Zr-MOFs was determined via the Freundlich model. DFT results suggest that the IND adsorption occurred at highly active sites such as O-linker, μ3-O-cluster, N-amine, and O-nitro via hydrogen and π-hydrogen bonds. Furthermore, the binding energy at each adsorption site in Zr-BDC-NH2 is higher than in Zr-BDC-NO2. In addition to the hydrogen acceptor bond, the π-hydrogen bond has also been analyzed through the electron density difference.