This paper is a review the polyoxometalate-based composite materials, including polyoxometalate incorporated Langmuir and Langmuir–Blodgett, layer-by-layer multilayers and novel honeycomb films, self-assembly structures of modified polyoxometalate complexes (e.g., onion-like structures, new inorganic–organic–inorganic vesicles, thermotropic and lyotropic liquid crystalline structures, gels), and amino acid- and protein-polyoxometalate nanorods and nanoparticles. Polyoxometalate-embedded layer-by-layer multilayer films show electrocatalytic or photochemical activity; and, novel photoluminescent honeycomb films templated by microwater droplets are reviewed. Inorganic–organic–inorganic hybrid vesicles display the potential as nano-switches. In addition, amino acid- and protein-polyoxometalate composite nanostructures indicate potential antimicrobial applications. Therefore, the polyoxometalate-based composite materials have promising applications in electrochemistry, photochemistry and biomedicine.