Magnetic covalent organic framework nanocomposite denoted as Fe3O4@TPBD-BTA with core-shell structure was fabricated via a simple template-mediated precipitation polymerization method at mild conditions. The polyimine network shell was created through the polymerization of N,N,N’,N’-tetrakis(p-aminophenyl)-p-phenylenediamine (TPBD) and biphenyl-3,3’,5,5’-tetracarbaldehyde (BTA) in tetrahydrofuran by the Schiff-base reaction. Featuring with large good solution dispersibility and high stability, the obtained Fe3O4@ TPBD-BTA exhibited high adsorption capacities and fast adsorption for aflatoxins (AFs). With the Fe3O4@ TPBD-BTA as sorbent, a magnetic solid-phase extraction high performance liquid chromatography-tandem mass spectrometry method was established for simultaneous adsorption and detection of two AFs in complex samples. The proposed method displayed favorable linearity, low limits of detection (0.006 5–0.008 2 μg/kg). The developed method has been applied for real sample analysis, with recoveries of 81.3%–87.4%. These results showed that Fe3O4@TPBD-BTA has a good application potential for the adsorption of AFs in milk and dairy products.