In order to study the influence of over-excavation thickness on internal force and displacement of retaining structure as well as surrounding environment, we simulate the excavation process of deep foundation pit by using Midas GTS software, hence obtaining the distributions of internal force of retaining structure, deformation and subsidence in the presence of different over-excavation thicknesses. The analysis results show that over-excavation thickness has big influence on internal force and displacement of retaining structure and ground subsidence, especially on horizontal displacement of retaining structure and ground settlement. Furthermore, affected by over-excavation, the maintaining effects of pile and anchor could not act in the same time, and soil deformation under the pile is big, which is unfavorable to the stability of foundation pit. Through the research, we can improve the design of deep foundation pit, and the results can be referenced for the design, construction and research of similar projects.