Toluene is a class of volatile organic compounds (VOCs) in the air that harm environmental quality and human health. To enhance the adsorption performance of adsorbents for toluene, based on the principle that unsaturated metal sites in MOFs can be replaced, nanoscale M@MIL-101(M represents Mg, Ca, Sr) with binuclear sites was prepared by a one-step solvothermal method. The second metal was successfully introduced into the topology of MIL-101 by partially substituting Cr sites. The results of the dynamic adsorption experiments showed that 20%Sr@MIL-101 exhibited the highest toluene adsorption capacity, which was about 60% higher than that of the undoped MIL-101. Analysis using a monolayer and multilayer model based on statistical physics theory indicated that the Sr/Cr binuclear sites could enhance the interaction strength of the adsorption system, promoting the adsorption of more layers of toluene molecules on the surface of MIL-101. Characterization and simulation together confirmed that constructing Sr/Cr binuclear sites in MIL-101 can cause significant redistribution of charge within the pores, enhancing the van der Waals interactions, π-π stacking interactions, hydrogen bonding, and Lewis acid-base interactions between the pore interior and the adsorbate molecules. Additionally, density functional theory (DFT) revealed that the adsorption sites of toluene in MIL-101 were distributed in a trigonal prism arrangement and were symmetrically aligned with a 180° rotation of the MIL-101 triangular cage.