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Polyoxometalates (POMs) has proved its advantage in constructing high-performance nanocomposite membranes such as catalytic membranes, adsorptive membranes, and forward osmosis membranes. However, it is challenging or tedious to characterize its distribution and effect on the membrane structures due to the equipment resolution limitation, discrete nano-scaled structures of POMs, and limited doping amount compared to the polymeric membrane matrix. In this paper, POMs-functionalized polyvinylidene fluoride (PVDF) membranes were fabricated by phase inversion combined with the sol-gel method, and electrochemical impedance spectroscopy (EIS) was utilized to analyze the nanocomposite membrane intrinsic properties. Through adjusting the additives in the sol-forming process, a set of membranes with varied intrinsic properties were developed accordingly. The wetting degree of the membranes related to the hydrophilic nature of the membrane surfaces had a crucial influence on the impedance measurements at the early stage. Through EIS analysis, it was demonstrated that the amination of the membrane matrix through (3-aminopropyl)trimethoxysilane (APTMS) treatment and the immobilization of POMs through electrostatic attraction would not generate new pore structures into the membrane and only alter the membrane surface roughness and composition. To my knowledge, it is the first time that EIS was utilized to characterize the hydrophilicity of the membranes and pore structures of the POMs-modified membranes. Our findings indicate that EIS can provide valuable information for probing the structures of other nano-materials-incorporated membranes.