To purify water from contaminents is essential for life on universe. Here, in this manuscript we introduces an innovative approach to overcome the intricate challenge of eliminating heavy metal ions and microplastics from water. We designed a mesoporous composite materials by synergistically integrating polyoxometalates (POMs) based ionic liquids with silica coated magnetic nanoparticles. The synthesis process initiates with the utilization of highly reduced molybdenum aggregates in polyoxometalate-ionic liquids, reinforced onto magnetic nanoparticles (POM–IL–MNPs). Crafted composites, including Q8[Mo64Ni8La6]@SiO2@Fe3O4, Q10[Mo64Ni8La6]@SiO2@Fe3O4, Q8[Mo176/Mo248]@SiO2@Fe3O4, and Q10[Mo176/Mo248]@SiO2@Fe3O4, are meticulously designed by substituting POM counter cations with long-chain alkyl-based quaternary ammonium salts. The ionic liquids and composites exhibit remarkable hydrophobicity and thermal stability due to large anions and long-chain organic counter cations. Comprehensive characterization, including FT–IR, UV–vis spectroscopy, TGA, DSC, CV, rheological study, elemental analysis, and ICP-AES, ensures a thorough investigation. Additional analyses, such as Powder X-ray diffraction (PXRD), SEM, EDX, DLS, N2 adsorption, and VSM, reveal amorphous crystallinity, distinctive surface morphology, and substantial specific surface area. Core shell structure of POM-IL-MNPs was determined by Transmision electron microscope (TEM), ICP-AES analysis demonstrates metal ion removal efficiencies from 87.35% to 99.98%, with DLS confirming 100% efficiency in PVC beads elimination. This research not only advances water decontamination but also provides valuable insights into designing and characterizing novel materials with promising environmental applications.