In this study, a novel and simple dual-phase solvent system for the improvement of extraction capability of magnetic molecularly imprinted polymer (MIP) beads in aqueous sample was proposed. The method integrated MIP extraction and micro-liquid-liquid extraction (micro-LLE) into only one step. A magnetic MIP beads using atrazine as template was synthesized, and was applied to aqueous media by adding micro-volume of n-hexane to form a co-extraction system. The magnetic MIP beads preferred to suspend in the organic phase, which shielded them from the disturbance of water molecule. The target analytes in the water sample was extracted into the organic phase by micro-LLE and then further bound to the solid-phase of magnetic MIP beads. The beads specificity was significantly improved with the imprinting efficiency of template increasing from 0.5 to 4.4, as compared with that in pure aqueous media. The extraction capacity, equilibration process and cross-selectivity of the MIP dual-phase solvent extraction system were investigated. The proposed method coupled with high-performance liquid chromatography was applied to the analysis of atrazine, simazine, propazine, simetryn, prometryne, ametryn and terbutryn in complicated sample such as tomato, strawberry juice and milk. The method is selective, sensitive and low organic solvent-consuming, and has potential to broaden the range of MIP application in biological and environmental sample.