Engineering of the interface for tuning the structural, functional, and electronic properties of materials via the formation of heterostructure composites exhibits immense potential in the current research scenario. This study reports a novel ternary composite synthesized by decoration of zero-dimensional Pd nanoparticles (NPs) and two-dimensional (2D) graphite oxide (GO) sheets in the UiO-66 metal-organic framework (MOF). A mixed matrix membrane was fabricated by incorporating this composite in the SPEEK polymer matrix, which exhibited higher selectivity compared to commercial Nafion 117. The synthesized composite and fabricated membranes were thoroughly characterized in terms of their chemical structures, microstructural morphologies, physicochemical, thermal, photo-electrochemical, and optical properties, ion-exchange capacity, proton conductivity, and methanol permeability. As per our knowledge, this is the first study which explores the effect of noble metal NPs and carbon 2D material simultaneously on the electronic structure of the MOF, resulting in improved selectivity. The electron-accepting nature of GO and surface plasmon resonance effect of Pd alter the energy band positions and scavenge the electrons, improving the proton conduction of the composite. The introduction of oxygen vacancies in lattice leads to efficient charge separation. The formation of a Schottky junction results in the localized electric field effect due to electron density fluctuation which aids in ion transport. The current study opens up a new route to overcome the major challenge associated with direct methanol fuel cells (DMFCs), that is, high/low methanol crossover by improving the proton conduction.