This paper introduced a wafer-scale fabrication approach for the preparation of nanochannels with high-aspect ratio (the ratio of the channel depth to its width). Edge lithography was used to pattern nanogaps in an aluminum film, which was functioned as deep reactive ion etching mask thereafter to form the nanochannel. Nanochannels with aspect ratio up to 172 and width down to 44 nm were successfully fabricated on a 4-inch Si wafer with width nonuniformity less than 13.6%. A microfluidic chip integrated with nanometer-sized filters was successfully fabricated by utilizing the present method for geometric-controllable nanoparticle packing.