Magnetron sputtering, vacuum evaporation and vacuum filtration are three methods to prepare carbon nanotube composite membranes. To investigate the effects of composite membranes’ structure on As(III) removal, morphologies and surface chemical properties of different composite membranes were determined by scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS) and X-ray diffraction (XRD). The impacts of different carbon nanotubes as well as the natural organic matter (NOM) on As(III) removal were also conducted. The results showed that MWCNT-OH and MWCNT-COOH composite membranes modified with nano-copper by magnetron sputtering and the Cu-based membrane fabricated by vacuum filtration had the highest removal efficiencies of As(III) in water, which could be up to 90%. However, the presence of natural organic matter in water inhibited the As(III) removal by these two nanocompoaite membranes.