Direct methane conversion into value-added liquid oxygenates is a holy-grail reaction. We modified MIL-100(Fe) MOFs materials with highly dispersed hydrophobic polydimethysiloxane nanoparticles to significantly enhance their water resistance. The C1 oxygenates demonstrated an impressive yield and selectivity of 83.13 mmol g cat.−1h−1 and 100 %, respectively, while achieving a turnover frequency of 332.5 h−1 for oxygenates. The results of spectroscopy characterization and theoretical calculation demonstrate that, during the hydrophobic modification process of the catalyst surface, the loss of some ligands leads to the formation of coordination unsaturated active sites (Fe(II) CUS). The Fe(II) CUS active sites can efficiently catalyze the cleavage of H2O2 to produce Fe(IV) = O active species with high Lewis acidity, those promote homolytic dissociation of methane C-H bond with a low energy barrier. This study expands the application of hydrophilic MOFs materials with coordinatively unsaturated metal sites in the heterogeneous catalytic reactions of liquid phase.