The sulfur removal process in diesel is one of the key technologies to produce clean energy using polyoxometalate (POM)-based catalyst with excellent catalytic active sites. Herein, a molecularly dispersed POM supported catalyst CNT@(C4mim)4VW12O40 (CNT@C4VW12) was designed by introducing imidazole ionic liquids (IL) [C4mim]Br as counterionic linkers for oxidation desulfurization (ODS). For the model oil, 100 % desulfurization rate and product selectivity can be achieved within 30 min, and it can be recycled for 5 times without obviously decrease. Moreover, CNT@C4VW12 also displayed excellent performance in real hydrotreated diesel with a removal rate of 97.4 %. Overall, a stable and molecularly dispersed catalyst was constructed by the cooperative effect of π-π stacking, hydrogen bonding and electrostatic force interaction among the CNT, [C4mim]+ and [VW12O40]4−, which would provide new inspirations for design of heterogeneous catalyst towards excellent ODS process.