Cost‐effective, non‐fluorinated polymer proton exchange membranes (PEMs) are highly desirable in emerging hydrogen fuel cells (FCs) technology; however, their low proton conductivities and poor chemical and dimension stabilities hinder their further development as alternatives to commercial Nafion®. Here, we report the inorganic‐organic hybridization strategy by facilely complexing commercial polymers, polyvinyl butyral (PVB), with inorganic molecular nanoparticles, H3PW12O40 (PW) via supramolecular interaction. The strong affinity among them endows the obtained nanocomposites amphiphilicity and further lead to phase separation for bi‐continuous structures with both inter‐connected proton transportation channels and robust polymer scaffold, enabling high proton conductivities, mechanical/dimension stability and barrier performance, and the H2/O2 FCs equipped with the composite PEM show promising power densities and long‐term stability. Interestingly, the hybrid PEM can be fabricated continuously in large scale at challenging ~10 μm thickness via typical tape casting technique originated from their facile complexing strategy and the hybrids’ excellent mechanical properties. This work not only provides potential material systems for commercial PEMs, but also raises interest for the research on hybrid composites for PEMs. The facile and cost‐effective hybridization strategy for proton exchange membranes (PEMs) design by blending 1 nm metal oxide clusters and polyvinyl butyral. The fuel cells equipped with the PEM show promising power densities and excellent durability that is on par with Nafion® and surpass the previously reported non‐fluorinated PEMs.