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[Display omitted] • A new method was proposed for preparing modified clays to control harmful algae blooms: single source with series modifications. • Kaolin that was modified by the new method could remove over 85% of Prorocentrum donghaiense cells. • Calcination, acid–alkali treatment, and the supplementation of raw kaolin during aging were indispensable processing steps in the new method. • A schematic mechanism of kaolin modification by the new method to obtain modified clay with high algal cell removal efficiency was illustrated. Modified clay (MC) is an effective and eco-friendly material that is widely used for controlling harmful algae blooms (HABs). In this study, a new method—single source with series modifications (SSSM)—was optimized for preparing a high-quality MC, and aluminum-rich clay (kaolin) was activated with a multistep treatment that included calcination (Cal), acid etching with alkali neutralization (Al–An), and raw clay supplementation and aging (RSA). The results showed that the removal efficiency of Prorocentrum donghaiense by the SSSM–MC exceeded 85%; Cal, Al–An, and RSA were indispensable processing steps for preparing the best MC with the SSSM method. The changes occurring in the mineral structure and chemical composition of kaolin treated by the different steps were characterized by FT-IR, XRD, 27Al-NMR and Al-Ferron. Surface dehydroxylation and disruption of the kaolin lattice after calcination significantly changed the aluminum structure from AlVI to AlV and AlIV. The relatively reactive AlV was readily released from the kaolin lattice with acid etching, and it subsequently reacted with external OH– to generate different polyhydroxyaluminum species because alkali was added during the Al–An step. The acidity of the above complex was further decreased by RSA, greatly increasing the yield of SSSM–MC while assuring the quality. [ABSTRACT FROM AUTHOR]