The invention relates to the technical field of semiconductor device preparation, and specifically relates to an MOS device atomic layer deposition in-situ preparation method. The preparation method comprises the following steps: cleaning a substrate, and placing the substrate into a selected region modification processing cavity; carrying out the selective modification of the surface of the substrate, and providing a nucleation center for the deposition and growth of a semiconductor material on the atomic layer; growing the semiconductor material at the modified part of the substrate in the atomic layer deposition cavity as a trench; carrying out the selective modification of the surface of the substrate, and providing a nucleation center for the deposition and growing of a high-k insulating material; growing the high-k insulating material at the modified part on the substrate in the atomic layer deposition cavity as a device gate medium layer; carrying out the selective modificationof the surface of the substrate, and providing a nucleation center for the deposition and growing of a metal layer; and growing the metal layer at the modified part on the substrate in the atomic layer deposition cavity as a device electrode. The method effectively improves the uniformity, stability and overall technological quality of the device.