Most protocols of sample preparation for isoflavone determination in soymilk and other liquid soybean products involves tedious freeze-drying and time-consuming extraction procedures. We report a facile and rapid magnetic solid-phase extraction (MSPE) of isoflavones from soymilk for subsequent high-performance liquid chromatography electrospray ionization tandem mass spectrometry (HPLC-ESI-MS/MS) analysis. The extraction was based on the selective binding of isoflavones to baicalin-functionalized core-shell magnetic nanoparticles (BMNPs). The proposed MSPE-HPLC-MS/MS analytical method had a linear calibration curve in the concentration range from 0.3 to 80 mg/L isoflavones. With the use of calycosin, an isomer of one of the isoflavones targeted as an internal standard, interday (5 days) precisions of the slope and intercept of the calibration curves were found to be in the range between 2.5% and 3.6% (RSD, n = 5). Six isoflavones, that is, daidzein, glycitein, genistein, daidzin, glycitin, and genistin were detected in commercial soymilk samples and quantified by the proposed analytical method. The results indicated that the method was useful for fast determination of isoflavones in soymilk and other liquid soybean products.