A phase-change nanolithography technique is developed to fabricate up to millions of two-/three-dimensional nanostructures (∼50 nm) over a large area at a high speed by combining femtosecond laser, microlens array, and wet etching process. Near-field scanning optical microscopy, electrical force microscopy, and atomic force microscopy were used to characterize optical and electrical properties of crystalline and amorphous states, respectively. Different reactions of both amorphous and crystalline areas in phase-change film to alkaline solution are demonstrated. Multiphoton absorption and ultrashort pulse contribute to nanostructure generation. This method opens up a route for nanodevice fabrication with phase-change material.