A silicon nanowire substrate having a structure in which a silicon nanowire film having a fine line-width is formed on a substrate, a method of manufacturing the same, and a method of manufacturing a thin film transistor using the same. The method of manufacturing the silicon nanowire substrate includes preparing a substrate, forming an insulating film on the substrate, forming a silicon film on the insulating film, patterning the insulating film and the silicon film into a strip shape, reducing the line-width of the insulating film by undercut etching at least one lateral side of the insulating film, and forming a self-aligned silicon nanowire film on an upper surface of the insulating film by melting and crystallizing the silicon film.