In recent years, red tides have increased worldwide in frequency, intensity, involving a higher number of causative species during the events. As the most commonly used method for control of red tides, modified clay (MC) was found to have differential ability to remove various red tide species. However, the underlying mechanisms have not yet been completely elucidated. In this study, the use of MC to remove three typical disaster-causing species, Aureococcus anophagefferens, Prorocentrum donghaiense and Heterosigma akashiwo, was investigated, and differential removal of these species was probed with insights into their biocellular properties and mechanical interactions. The results showed that removal efficiencies of the three species by MC decreased in the order P. donghaiense > A. anophagefferens > H. akashiwo, while the sedimentation rates decreased in the order H. akashiwo > P. donghaiense > A. anophagefferens. Analyses of the cell surface properties and redundancy analysis (RDA) revealed that the highest surface zeta potential of -5.32±0.39 mV made P. donghaiense the most easily removed species; the smallest cell size of 3.30±0.03 μm facilitated the removal of A. anophagefferens; and the highest hydrophobicity with a H2O surface contact angle of 98.50±4.31° made the removal of H. akashiwo difficult. X-ray photoelectron spectroscopy (XPS) data indicated that the electronegativity of P. donghaiense was caused by carboxyl groups and phosphodiester groups, and the hydrophobicity of H. akashiwo was associated with a high C-(C, H) content on the cell surface. According to the extended Derjaguin, Landau, Verwey, and Overbeek (ex-DLVO) theory calculation, differences in the interaction energies between MC and the three red tide species effectively explained their different sedimentation rates. In addition, the degree of oxidative damage caused by MC to the three red tide species differed, which also affected the removal of red tide organisms.