Molecularly imprinting technique was combined with magnetic nanoparticles to synthesize molecularly imprinted polymer‐encapsulated particles for selective removal and efficient separation of estrogenic compounds from water. The core‐shell‐structured particles were successfully prepared by a novel 2‐h ultrasonication‐assisted synthesis in a mixture of water and organic solvent using dual‐layer surfactant‐modified magnetic particles as core, the most physiologically active estrogenic compound (17β‐estradiol) as template, and widely adapted methacrylic acid as functional monomer. Ultraviolet–visible spectroscopy, Fourier transform infrared spectroscopy, scanning electron microscopy, and magnetic separation were used to characterize the particles. High‐performance liquid chromatography–tandem mass spectrometry was used for quantitative binding performance analysis at low‐nanogram per milliliter levels. The particles exhibited satisfactory recognition of 17β‐estradiol in water. They possessed great potential for rapid, cost‐effective, and efficient separation of estrogenic compounds from aqueous environment with specificity. POLYM. ENG. SCI., 2012. © 2012 Society of Plastics Engineers