A novel method was developed for the purification of two typical diarrhetic shellfish poisoning toxins from toxin-producing marine microalgae using macroporous resin, high-speed countercurrent chromatography-mass spectrometry, and semipreparative high-performance liquid chromatography-mass spectrometry. Analytical high-performance liquid chromatography-mass spectrometry was used for identification and purity analysis of okadaic acid and dinophysistoxin-1 because they exhibit no visible or ultraviolet absorption. First, four kinds of macroporous resins were investigated, and HP-20 macroporous resin was selected for the preenrichment and cleanup of the two target toxins. Second, the resin-purified sample was further purified using high-speed countercurrent chromatography coupled with a mass spectrometer. The purities of the obtained okadaic acid and dinophysistoxin-1 were 89.0 and 83.0%, respectively, as determined through analytical high-performance liquid chromatography-mass spectrometry. Finally, further purification was carried out using semipreparative high-performance liquid chromatography with mass spectrometry, and the purities of the final okadaic acid and dinophysistoxin-1 products were both over 98.0% based on the analytical high-performance liquid chromatography-mass spectrometry chromatograms and fraction spectra. This work demonstrates that the proposed purification process is a powerful method for the preparation of high-purity okadaic acid and dinophysistoxin-1 from toxin-producing marine microalgae. Moreover, it is particularly important for the purification and preparation of minor toxins that exhibit no visible or ultraviolet absorption from harmful marine algae.