We describe a new method for fabrication of three-dimensional layered structure in large area by a lithographic technique with the Talbot effect. The Talbot effect is three-dimensional phenomena of diffraction and interference of high order diffraction light using a grating mask with sub-micrometer frequency. By using a grating with about 800 nm period, it was successful to fabricate three-dimensional nanostructures on SU-8 photoresist in a millimeter region. The typical nanostructure has 300 x 500 nm x 2 mm hole with three layers. Furthermore, the proposed method using the combination of the Talbot effect and wave-front control was demonstrated for controlling horizontal periodicity.