We report the design, synthesis, and assembly of functionalized carbon nanotubes (f-CNTs) in the absence of other templates by using a polysiloxane quaternary ammonium salt. Specifically, the perpendicular organic coating has a depth of ca. 3.2 nm and its hydrophobic nature provides the hydrophobic interactions (driving force) between near-neighbor CNTs. Once a complete coverage (ca. 100 %) of CNTs is achieved, the upper-layer nanotubes can spontaneously and readily interact with the sublayer tubes to assemble into oriented nanostructures with a tube distance of 26 nm along the tube axis. Therefore, the spontaneous assembly of f-CNTs in aqueous solution becomes possible without the help of other templates. Additionally, further investigations suggest that it is easier to obtain arrayed nanostructures with straight f-CNTs with 100 % coverage than with curved ones. Our strategy seems very attractive because the aligned CNT array can be achieved through simple control of the chemical functionalization of the nanotubes. This offers us a valuable insight into the bottom-up design of f-CNTs, one-dimensional nanostructures, and building blocks for supramolecular chemistry and nanotechnology.