Objective To develop a multiwalled carbon nanotube (MSPE) method coupled with ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS)by preparing a magnetic multiwall carbon nanotube composite nanoparticles modified with 3-aminobenzeneboronic acid for simultaneous determination of 9 kinds of microcystins in aquatic products. Methods Magnetic multiwall carbon nanotubes (Fe₃O₄/MWCNTs) composite nanoparticles were prepared by hydrothermal synthesis. Then, the 3-aminobenzeneboronic acid was modified on the prepared magnetic carbon nanotubes through the chemical oxidation method. The nanoparticles have been characterized by transmission electron microscopy and infrared spectroscopy. The main factors influencing the extraction efficiency were optimized. And then a preprocessing method with acetic acid-PBS buffer solution-methanol (2∶49∶49, V/V) was selected as the extraction solution, and 50 mg magnetic nanomaterials were used for extraction for 15 min, 5% ammoniated methanol was used as the eluting solvent within 10 min. Results The calibration curves of microcystins showed a good linearity in the range of 5-200 ng/mL with correlation coefficients above 0.998.The detection limits(LOD)of the method were in the range of 0.15-8.71 μg/kg. The average relative recoveries of three spiked levels ranged from 91.8% to 103.2% with the relative standard deviations of 3.1%-9.5%. Conclusion The method has the characteristics of simple pretreatment, high sensitivity and high recoveries, superior to national standard method. It could simultaneously determine 9 kinds of microcystins in aquatic products and provides a powerful technical guarantee for the monitoring of microcystins in aquatic products.