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In the pursuit of heterogeneous catalysts with high reactivity, metal organic framework (MOF) nanomaterials have received tremendous attentions. However, many MOF catalysts especially Fe-based MOFs need to be utilized immediately after synthesis or being activated using high temperature, because of the easy loss of reactivity in humid environments resulting from the occupation of active Fe sites by water molecules. Here, we describe an inspiring strategy of growing MIL-101-Fe nanoparticles inside the three-dimensional confined space of graphene aerogel (GA), generating shapeable GA/MIL-101-Fe nanocomposite convenient for practical use. Compared to MIL-101-Fe, GA/MIL-101-Fe as catalyst demonstrates much higher reactivity in Fenton-like reaction, attributing to smaller MIL-101-Fe particle size, presence of active Fe(II) sites, and abundant defects in GA. Strikingly, the weakly hydrophobic nature of the composite greatly inhibits the loss of catalytic reactivity after being stored in humid air and accelerates the recovery of reactivity in mild temperature, by resisting the entrance of water molecules and helping to exclude water molecules. This work demonstrates that a delicate design of nanocomposite structure could not only improve the reactivity of the catalytic component, but also overcome its intrinsic drawback by taking advantage of the properties of host. We hope this functional nanoconfinement strategy could be extended to more scenarios in other fields.