Herein, we report the adsorbate behavior in individual local pores of MIL-101, which is a metal-organic framework (MOF) with two heterogeneous mesopores and different metal sites, by combining adsorbate isotherms and in situ crystallography profiles. The in situ mapping shows that the substrate-adsorbate interaction affects the initial adsorption and pore condensation steps. The monolayer adsorption gradient changes greatly depending on the framework metal-adsorbate attraction force. Also, broad inflection points are found in adsorption isotherms, and the initial shape depends on the different metals. Besides, the capillary condensation at a pore draws adsorbates from other local pores. This leads to the local negative uptake behavior in individual pore isotherms. At higher pressure, they move to a larger space, whereas in a relatively low-pressure range the attraction force between the MOF framework and guest molecule influences the amount of rearranged guest molecules. Furthermore, the origin of the characteristic adsorption behavior based on the metals constituting the MOFs and the relative strength of substrate-adsorbate and adsorbate-adsorbate interactions are elucidated through the combined study of electron densities in pores, electron paramagnetic resonance spectroscopy spectra, and density functional theory and Monte Carlo simulations to uncover the previously veiled information on adsorption behavior.