Membrane separation technology is widely explored for various applications, such as water desalination and wastewater treatment, which can alleviate the global issue of fresh water scarcity. Specifically, carbon nanotubes (CNTs)-based composite membranes are increasingly of interest due to the combined merits of CNTs and membrane separation, offering enhanced membrane properties. This article first briefly discusses fabrication and growth mechanisms, characterization and functionalization techniques of CNTs, and then reviews the fabrication methods for CNTs-based composite membranes in detail. The applications of CNTs-based composite membranes in water treatment are comprehensively reviewed, including seawater or brine desalination, oil-water separation, removal of heavy metal ions and emerging pollutants as well as membrane separation coupled with assistant techniques. Furthermore, the future direction and perspective for CNTs-based composite membranes are also briefly outlined.