A [BMIM]PF6 ion liquid (IL)-assisted synthesis of a rutin imprinted monolith (RIM) was carried out in an in-situ polymerization method. Bi-functional monomers and a ternary porogen containing IL was used for the RIM preparation and a L9(33) orthogonal factor design performed. Scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FT-IR) and N2 adsorption method was for structural characterization of the RIMs. The monolith was directly used as stationary phase in liquid chromatography to test the retention selectivity, adsorption capacity and extraction application. The optimized porogen consists of 900 μL DMF, 144 μL ACN and 216 μL IL. The monolith RIM-13 obtained under the optimized conditions possessed improved adsorption performance, with a dynamic adsorption capacity of 6.695 mg/g, an imprinting efficiency of 4.841 and a selectivity α value of 4.821. Additionally, this monolith had also higher specific surface area, pore volume and permeability than that obtained without IL and the homogeneity of the imprint sites could be improved by using IL. When the RIM-13 was applied to the separation and purification of rutin from tartary buckwheat, a rutin product with a purity higher than 92 % can be obtained by one cycle. This molecular imprint solid-phase extraction (MI-SPE) is of potency to be applied to preparative-scale separation of other natural products.