The functionalized organic polymer monolithic column was synthesized in a stainless steel column (4.6 mm i.d. × 100 mm). 1,6-Hexanediol dimethacrylate and 1-allyl-3-methylimidazole chloride were designed as bifunctional monomers, methanol and dodecanol were used as porogens, and azobisisobutyronitrile was used as initiator. The prepared pre-polymerization solution was polymerized in a water bath at 60 °C. In the preparation process, the resolution and peak shape of phenanthrene, biphenyl and benzene were chosen as indicators to optimize the addition amount of 1-allyl-3-methylimidazole chloride. The monolithic column was used to separate neutral, phenolic and aniline compounds, and then the performance was evaluated. The results show the stationary phase permeability K = 3.49 × 10–12/m2, and the resolution R > 1.5 for various compounds. In addition, the retention mechanism of the monolithic column may be typical reversed-phase chromatography. The successful preparation of the monolithic column proves the hypothesis that the addition of ionic liquid can reduce the column pressure, and the prepared monolithic material can successfully separate three types of small molecule compounds. Ionic liquids can be regarded as a good modifier for organic polymer monolithic column.