Halloysite is a curly layered aluminosilicate clay with abundant reserves and low price. It can be used to prepare clay composite materials, which can be applied to biomedicine and wastewater treatment fields. The inner and outer surfaces of halloysite are composed of Al-OH octahedrons and Si-O tetrahedrons, respectively, which ionize in the opposite way in water, resulting in opposite charges on the inner and outer surfaces of halloysite nanotubes. Therefore, the selective modification of halloysite can be achieved by chemical or electrostatic adsorption. In addition, as halloysite has a nanotube structure, it can be used to construct rough structures in micro- or nano-scale. By incorporation with the low-surface-energy materials, the hydrophobic halloysite-based composite materials could be prepared for self-clean and oil-water separation. This review introduces the design strategies of the hydrophobic structures based on halloysite, and summarizes their applications in oil-water separation, hydrophobic coating, loading and sustained release of drug molecules.