Four new types of amphiphilic polyoxometalate-based poly(ionic liquid) (PDB-PMo, PDO-PMo, PDD-PMo and PDH-PMo) were prepared by ion exchange between poly(ionic liquid) (PIL) and H3PMo12O40 (HPMo), where PIL are copolymerized by hydrophilic 3,3′-methylenebis(1-vinylimidazol) bromine and hydrophobic [3–alkyl–1–vinylimidazolium] bromine (alkyl = C4, PDBBr; alkyl = C8, PDOBr; alkyl = C12, PDDBr and alkyl = C16, PDHBr). Among them, the desulfurization rate of PDD-PMo can reach 100% within a wide temperature range of 0–50 °C, especially at 0 °C, DBT can be completely removed within 100 min. The influences of reaction temperature, molar ratio of H2O2/S, catalyst dosage and different sulfur-containing compounds were investigated. The kinetic study shows that the apparent activation energy of the DBT oxidation reaction is 36.73 ± 1.42 kJ/mol. In addition, EPR analysis and the free radical quenching experiment proved that both active radicals O2•− and HO• played an active role in the oxidative desulfurization (ODS) reaction system and proposed a reasonable reaction mechanism. The introduction of hydrophilic IL monomer is also an efficient strategy to construct amphiphilic polyoxometalate-based poly(ionic liquid), which further implements ultra-deep desulfurization.