The double sidewall guide pit and centre cross diagram (CRD) methods are often used for the construction of large-section tunnels through water-rich fault fracture zones due to their long construction time and high construction cost. To shorten the construction period and save costs, the top heading and benching method (HB) and centre diaphragm (CD) can be chosen for construction. The construction parameters of the step and CD methods are optimized to ensure the surrounding rock stability and tunnel safety. By relying on the Tongzi Tunnel, we simulate the excavation of different step heights in the construction of the top heading and benching method (HB) and CD methods through numerical simulation, the laws of tunnel vault settlement, and changes in the surrounding rock stress, initial support axial force, bending moment and safety factor. The study shows that as the height of the upper step increases, the settlement of the vault and the convergence of the periphery increase, the initial support safety factor decreases, and the plastic zone of the surrounding rock increases at 30 m from the target face. The step height for the top heading and benching method (HB) of construction is optimized as follows. The ratios of the upper, middle and lower step heights are 0.45H, 0.35H and 0.2H, respectively. The CD method construction step height is optimized to the left (right) upper and left (right) lower step height ratios of 0.5H and 0.5H, respectively.