In order to study the deformation characteristics of the retaining structure under the coupled effect of excavation and dewatering in the affected area of fault zones, this paper takes a deep excavation project in the F1322 fault zone influence area in Shenzhen as an example. The research methods of theoretical analysis, numerical simulation and field measurement are used to conduct in-depth research on the deformation of the retaining structure caused by the excavation and dewatering of the foundation pit. The results show that considering the coupled effect of dewatering in the foundation pit, the energy method based on elastic theory is more accurate in solving the deformation of the retaining pile. By comparing and analyzing the theoretical calculation results, numerical analysis results, and field measurement values, we found that the numerical laws of the three are basically the same. Simplified calculations that only consider rotational deformation and ignore the translational deformation of the wall lead to large deviations between the theoretical calculation results and the measured values of the wall bottom deformation. In order to reduce the deviation between numerical results and measured values, the construction of the foundation pit should strictly adopt measures such as “sectional excavation, avoiding peripheral loads, and optimizing construction deployment”, strengthen construction monitoring, and reduce the impact on the deformation of the retaining pile. The maximum deformation growth rate k (ΔSmax/Δ) of the retaining pile decreases approximately exponentially with the increase of the structural stiffness parameters (E and I) and the embedment ratio within a certain range. The sensitivity analysis of the lateral displacement of the retaining pile to different geological parameters is conducted, and the sensitivity factors of the geological parameters to the deformation of the retaining structure are obtained, namely the maximum internal friction angle, followed by the cohesion, and the elastic modulus is the smallest. Based on the original design plan, an optimization of the excavation design is proposed by reducing the stiffness of the support structure. Therefore, the research findings in this paper have significant theoretical and practical implications for the engineering design of excavation projects located in fault zones. By optimizing the excavation support system, not only can standardized construction procedures be achieved, but also investment costs can be reduced, and construction time shortened, which fully aligns with the current safety, economic, and sustainable design principles of excavation projects aiming to conserve resources.