InAs/GaAs quantum dots (QDs) have been extensively applied to high-performance optoelectronic devices due to their unique physical properties. In order to exploit the potential advantages of these QD-devices, it is necessary to control the QDs in density, uniformity and nucleation sites. In this work, a novel research of in-situ pulsed laser modifying InAs wetting layer is carried out to explore a new controllable method of growing InAs/GaAs(001) QDs based on a specially designed molecular beam epitaxy (MBE) system equipped with laser viewports. Firstly, a 300 nm GaAs buffer layer is grown on GaAs (001) substrate at 580 ℃ and the temperature decreases to 480 ℃ to deposit InAs. As soon as the amount of InAs deposition reaches 0.9 ML, a single laser pulse ( =355 nm, pulse duration ～ 10 ns) with an energy intensity of ～ 40.5 mJ/cm2 is in-situ introduced to irradiate the surface. Then, the sample is taken out and then its surface modification is immediately evaluated by atomic force microscope measurement. Atomic layer removal nano-holes elongated in the direction, and a surface density of ～2.0109 cm-2 are observed on the wetting layer. We attribute the morphology change to being due to laser-induced atom desorption. Because indium atoms should be easily desorbed away at substrate temperature of 480 ℃ during the laser irradiation, some vacancy defects are created. Then atoms adjacent to those defects would become weakly bounded, resulting in preferential desorption around the defect sites in sequence. Therefore, atomic layer removal is intensified by such a kind of chain effect and finally nano-holes are developed on the surface. In order to make clear how these nano holes of special kind influence the InAs/GaAs (001) QD growth, we perform another study by continuously depositing the InAs after the irradiation at the same thickness of 0.9 ML. It is found that when 1.7 ML InAs is deposited, QDs start to nucleate into some nano-holes and then are further deposited with an InAs coverage of 1.9 MLs, all the nano holes would be completely nucleated by QDs with a good uniformity, and there are no QDs in the remaining area. Such an effect of QD preferential nucleation in nano-holes could be explained by the following two causes. Firstly, adsorbed indium atoms tend to immigrate into nano-holes for lower surface energy induced by the concave surface curvature. The enhanced accumulation of Indium is in favor of the preferential nucleation of QDs in nano-holes. On the other hand, QD growth in areas outside the nano holes is depressed for indium desorption in pulsed laser irradiation process. In conclusion, our studies of in-situ laser-induced surface modification reported here provide a potential solution of controllable InAs/GaAs (001) QD growth.