In this paper, during InAs/GaAs (001) quantum dot molecular beam epitaxy growth, four-beam pulsed laser-interference was used to in-situ irradiate on the wetting layer with an InAs coverage of 1.1 monolayer. Significant atomic layer removal and periodic nanostructures including nanoholes and nanoislands were obtained. These periodic nanostructures had a significant influence on quantum dot growth. Especially for the structure of nano-island, quantum dots preferentially nucleated at the edges of them. When the nano-island size becomes small enough, ordered quantum dot arrays are directly achieved on smooth GaAs surface with a follow-up InAs deposition accompanied by the disappearance of the nanoislands. This finding provides a potential technique leading to site-controlled and defect-free quantum dot fabrication.