In order to investigate the influence of the secondary phase trench construction of diaphragm walls with rigid joints on the deformation and stress of the primary I-shaped steel boxes, the north anchorage diaphragm wall of the south channel bridge of the Zhangjinggao Yangtze River Bridge was taken as the engineering case. Field measurements and numerical simulations were used to analyze the mechanical response of the primary steel boxes during the two key stages: trench milling and concrete pouring of the secondary phase. The results show that after the milling of the secondary trench, the primary steel boxes deform towards the secondary trench. The measured maximum displacement is 21.3 mm, and the maximum vertical tensile stress is 19.8 MPa, while the calculated values are 16.5 mm and 16.6 MPa, respectively. After concrete pouring, the steel boxes deform in the opposite direction. The measured maximum displacement is 4.5 mm, and the maximum compressive stress is -17.0 MPa, while the calculated values are 6.8 mm and -17.8 MPa, respectively. After superimposing the two working conditions, the steel boxes ultimately deform towards the secondary trench side. The measured maximum displacement is 16.5 mm, and the maximum tensile stress is about 3 MPa, while the calculated values are 12 mm and 5.7 MPa, respectively. When the cross-sectional area of the core concrete in the steel boxes is doubled, the deformation and stress in the two stages are reduced by 60% to 70%. In the final state, the deformation is reduced by 68.3% and the stress is reduced by 38.6%. It is concluded that the construction of the secondary phase has a significant influence on the stress and deformation of the primary steel boxes. Monitoring and control need to be strengthened during construction. The bending resistance of the I-shaped steel boxes also needs to be improved in the design phase of similar ultra-deep diaphragm walls.