•Fe3O4@SiO2@MOF core–shell magnetic microspheres were prepared as MSPE sorbent.•Fe3O4@SiO2@MOF core–shell magnetic microspheres were used for MSPE of polar analytes.•Fe3O4@SiO2@MOF core–shell magnetic microspheres achieved high extraction efficiency. Fe3O4@SiO2@UiO-66 core–shell magnetic microspheres were synthesized and characterized by transmission electron microscopy, scanning electron microscopy, X-ray diffraction, Fourier transform infrared spectrometry, vibrating sample magnetometry, nitrogen adsorption porosimetry and zeta potential analyzer. The synthesized Fe3O4@SiO2@UiO-66 microspheres were first used for magnetic solid-phase extraction (MSPE) of domoic acid (DA) in shellfish samples. Combined with high performance liquid chromatography–tandem mass spectrometry (HPLC–MS/MS), a fast, simple and sensitive method for the determination of DA was established successfully. Under the optimized conditions, the developed method showed short analysis time, good linearity (r2=0.9990), low limit of detection (1.45pgmL−1; S/N=3:1), low limit of quantification (4.82pgmL−1; S/N=10:1), and good extraction repeatability (RSD≤5.0%; n=5). Real shellfish samples were processed using the developed method, and trace level of DA was detected. The results demonstrate that Fe3O4@SiO2@UiO-66 core–shell magnetic microspheres are the promising sorbents for rapid and efficient extraction of polar analytes from complex biological samples.