Take one subway station of Chongqing rail transit as background, 3D FEM models of sequential excavating to large-section and ultra-deep shafts under complicated environment were set up, and influence of shaft construction to the stability of shaft wall rock, slab-pile walls, high-voltage tower foundation and intersection of shafts and air flues was analyzed. The analysis result showed: wall rock displacement near the contour line of shaft and air flue changed significantly and the maximum displacement was 10.84 mm; vertical displacement caused by shaft and air flue excavating affected ground surface and the maximum ground surface settlement was 20 mm; shaft excavating brought large stress to shaft walls and the maximum vertical stress was 2.94 MPa; plastic zone of wall rock mainly distributed in the junction of shaft and air flue, outward excavation contour line for 6-10 m, and the distribution range was large. The maximum principal stress of shaft and air flue during initial support at the junction of air flue vault and curve walls was large, and the maximum stress was 6.09 MPa; the maximum and minimum principal stress of slab-pile retaining walls before shaft and air flue excavating was -1.60 MPa and 0.32 MPa, then increased to -1.78 MPa and 0.63 MPa respectively after excavating, additionally, shear failure would not happen; the maximum displacements from X-scale, Y-scale and Z-scale of tower’s foundation were 0.32 mm, 0.86 mm and 1.20 mm respectively. Furthermore, the difference of inhomogeneous deformation was small, and shaft construction had no effect to high-voltage towers.