A sensitive and efficient magnetic amino modified multi-walled carbon nanotubes (m-MWCNT-NH2)-based magnetic dispersive solid-phase extraction (m-dSPE) coupled with hydrophilic interaction liquid chromatography–tandem mass spectrometry (HILIC-MS/MS) strategy is reported for the simultaneous determination of 13 paralytic shellfish toxins (PSTs) in bivalve mollusks. The samples were extracted twice with 1% acetic acid and purified using optimized m-dSPE procedures with Fe3O4 coated MWCNT-NH2 composites as magnetic adsorbents. The adsorbed PSTs on the m-MWCNT-NH2 adsorbents were separated using a Ni-coated neodymium magnet and subsequently eluted with 2 mL water–acetonitrile–acetic acid (80:20:1, v/v/v) and analyzed by HILIC-MS/MS. The correlation coefficients (r) of the targeted toxins obtained in matrix-matched external standard curves were from 0.997 to 0.999. The PSTs were acquired and quantified in the multiple reaction-monitoring mode and the limits of detection and quantitation in bivalve mollusks were 1.10 to 4.51 μg/kg and 3.67 to 13.5 μg/kg, respectively. Spiked recoveries at three concentrations in negative samples were from 73.4% to 92.5% with precision less than 10.6%. The method validation was in accordance with 2002/657/EC guidelines and method application in commercial bivalve mollusk samples. The developed method was rapid, convenient and economical for the determination of the targeted toxins.