The subway shield tunnel construction is about to pass through a proposed seven-storey public three-dimensional garage project, and there are conflicts and mutual influences between the two projects. It is necessary to ensure the safe tunneling of subway tunnels, as well as the safe construction and operation of three-dimensional garages. It is particularly important to analyze the impact of the construction sequence on the safety of the project and optimize the construction sequence to promote the implementation of the project. Three-dimensional finite element software is used to carry out numerical simulation calculation on different construction time sequence of subway shield tunnel crossing underneath the multi-level garage, and the static force behavior of the multi-level garage structure and subway tunnel structure is analyzed. The results show that it is advantageous for the force and deformation of shield tunnel structure to construct the multi-level garage first, the multi-level garage is favorable for the stress of the shield tunnel structure in the early construction, and the design floor live load of the multi-level garage must be adjusted. The analysis results could provide an important means and effective basis for implementing the safety assessment of complex structure projects.