Polyionic liquids(PILs) have the characteristics of non-volatile, high thermal stability and excellent performance. Because of its strong solubility and molecular recognition ability, it has broad application prospects in the field of azeotropic separation.. In this manuscript, based on COSMO calculation, methylimidazole ionic liquid(ILs) with strong hydrophilic anions was selected as extractant to separate trioxane water and ethanol water azeotropic systems. The screening results were verified by vapor–liquid equilibrium experiments. It was found that [VMIm][DMP] could separate trioxane water and ethanol water azeotropic systems effectively at the same time. In the separation of azeotropes, because the ILs extractant has too strong interaction with H2O and the thermal stability is not satisfactory, the recovery energy consumption is high and the heat loss is serious. In this work, [VMIm][DMP] and [VEIm][DEP] were selected as ionic liquid monomers (ILM), and PILs were prepared by the reversible addition-fragmentation chain transfer (RAFT) method. The molecular dynamics (MD) simulation is performed to study the interactions between the solvent molecules and ILs/PILs, in order to investigate the separation mechanism at the molecular level. The study found that increasing the degree of polymerization is beneficial to improve the thermal stability of PILs and relative volatility of trioxane and ethanol, and the influence of degree of polymerization and alkyl side chain length on the hydrogen bond strength of PILs-H2O, PILs-trioxane and PILs-ethanol were studied by MD simulation.