A novel magnetic solid-phase extraction (MSPE) method based on mixed hemimicelles of room temperature ionic liquids (RTILs) coated Fe3O4/SiO2 nanoparticles (NPs) was developed for simultaneous extraction of trace amounts of flavonoids in bio-matrix samples. A comparative study on the use of RTILs (C16mimBr) and CTAB-coated Fe3O4/SiO2 NPs as sorbents was presented. Owing to bigger adsorption amounts for analytes, RTILs-coated Fe3O4/SiO2 NPs was selected as MSPE materials and three analytes luteolin, quercetin and kaempferol can be quantitatively extracted and simultaneously determined coupled with high performance liquid chromatography (HPLC) in urine samples. No interferences were caused by proteins or endogenous compounds. Good linearity (R2>0.9993) for all calibration curves was obtained, and the limits of detection (LOD) for luteolin, quercetin and kaempferol were 0.10ng/mL, 0.50ng/mL and 0.20ng/mL in urine samples, respectively. Satisfactory recoveries (93.5–97.6%, 90.1–95.4% and 93.3–96.6% for luteolin, quercetin and kaempferol) in biological matrices were achieved. It was notable that while using a small amount of Fe3O4/SiO2 NPs (4.0mg) and C16mimBr (1.0mg), satisfactory preconcentration factors and extraction recoveries for the three flavonoids were obtained. To the best of our knowledge, this is the first time a mixed hemimicelles MSPE method based on RTILs and Fe3O4/SiO2 NPs magnetic separation has ever been used for pretreatment of complex biological samples.