Given that hydrogen production often involves impurities such as CO2, CH4, H2O, and alkanes, hydrogen purification is crucial for global green energy applications. Mixed matrix membranes (MMMs) using metal-organic framework (MOF) materials offer a non-thermal, energy-efficient method for hydrogen purification. These membranes have controllable structures and promote environmental sustainability. However, challenges such as filler aggregation and matrix-filler incompatibility during the preparation of MOF-MMMs are difficult to avoid and can adversely affect separation performance. In this study, 4-(trifluoromethyl) benzoic acid (4-TFMBA) was introduced in situ to grow synchronously with polyvinyl pyrrolidone (PVP) on UiO-66-NH2, forming a hydrophobic bifunctional nanoparticle composite, PVP-Zr-MOF-F. Furthermore, in situ loading of PVP-Zr-MOF-F onto a PVDF polymer matrix was achieved using a wet method and the NIPS technique to prepare PVP-Zr-MOF-F@PVDF. The introduction of 4-TFMBA, with highly electronegative F atoms, enhances hydrophobicity and increases H2 affinity through polarization and hydrogen bonding induced by C–F bonds. PVP promotes the formation of smaller Zr-MOF particles, increases the proportion of small pores, prevents aggregation, and acts as a pore-forming agent, facilitating the in situ loading and dispersion of PVP-Zr-MOF-F within PVDF chains. This bifunctionalization not only improves the compatibility and dispersion of the nanofillers but also increases the number of small pores, enhancing van der Waals forces and confinement effects on H2 molecules, making it suitable for gas separation under humid conditions. The results indicate that the H2 permeance of PVP2–Zr-MOF-F@PVDF can reach 114,735 GPU, with selectivities of 19, 21, 24, and 120 for H2/CO2, H2/CH4, H2/C2H4, and H2/n-C6H14, respectively, surpassing the 2008 Robeson's upper bound. Notably, under high humidity conditions, the selectivities for H2/CO2, H2/CH4, and H2/n-C6H14 are 1566 %, 1891 %, and 3264 % higher than those of the original PVDF membrane, achieving high selectivity separation. Additionally, after repetitive experiments with varying humidity, the membrane's selectivity remained almost unchanged, demonstrating the high hydrothermal stability of PVP2–Zr-MOF-F@PVDF. This research provides a new reference for hydrogen purification and holds significant implications for the sustainable development of green energy.