A novel flocculation strategy for simultaneously removing Microcystis aeruginosa and algal organic matter (AOM) was proposed using chitosan-amphoteric starch (C-A) dual flocculants in an efficient, cost-effective and ecologically friendly way, providing new insights for harmful algal blooms (HABs) control. A dual-functional starch-based flocculant, amphoteric starch (AS) with high anion degree of substitution (DSA) and cation degree of substitution (DSC), was prepared using a cationic moiety of 3-chloro-2-hydroxypropyltrimethylammonium chloride (CTA) coupled with an anion moiety of chloroacetic acid onto the backbone of starch simultaneously. In combination of the results of FTIR, XPS, 1H NMR, 13C NMR, GPC, EA, TGA and SEM, it was evidenced that the successfully synthesized AS with excellent structural characteristics contributed to the enhanced flocculation of M. aeruginosa. Furthermore, the novel C-A dual flocculants could achieve not only the removal of >99.3 % of M. aeruginosa, but also the efficacious flocculation of algal organic matter (AOM) at optimal concentration of (0.8:24) mg/L, within a wide pH range of 3–11. The analysis of zeta potential and cellular morphology revealed that the dual effects of both enhanced charge neutralization and notable netting-bridging played a vital role in efficient M. aeruginosa removal.