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A high adsorption capacity of BPA up to 209.9 mg/g that was better than common 2D-COFs was achieved, and the sensitive MSPE-LC-MS method with wide linear range (10-5000 pg/mL), low detection limit (4 pg/mL, S/N = 3) was built. Satisfactory recoveries of BPA as 93.8 ± 1.4%-101.4 ± 5.1% (n = 3) and 100.4 ± 1.9% ~ 107.3 ± 1.2% (n = 3) were obtained in milk and river water samples, respectively. This work demonstrates the promising application of Fe3O4@3D COF as efficient adsorbents of trace BPA, and opens up a new access for the efficient