A maintenance drainage well has a large scale, deep excavation depth, complex formation conditions and boulders. In order to ensure the stability of the excavation of the deep foundation pit and improve the construction efficiency, the whole process of the excavation of the ultra-deep shaft foundation pit is simulated by using the three-dimensional numerical simulation software FLAC3D, and the stress and deformation characteristics of the ultra-deep shaft structure under five different layered excavation thicknesses are analyzed. The results show that: 1) The maximum hoop stress and maximum horizontal displacement of the diaphragm wall increase with the increase of layered excavation thickness, and the stress and deformation spurt occur within the soft rock strata, and the stress and abrupt deformation deceleration occur within the hard rock stratum; 2) Taking the maximum hoop stress and maximum horizontal displacement of the diaphragm wall under unlined excavation as the reference standard, the thickness range of single-layer excavation is 3~4 m, which has a good restraining effect on the displacement of the diaphragm wall, and it is recommended that the layered thickness of 3 m should be used for soil excavation and soft rock excavation in actual engineering, and the layered thickness of 4 m should be used for the excavation of hard rock part of the formation. The results can provide guidance for on-site shaft construction and provide reference for ultra-deep shaft excavation under similar background.