The structural requirements of buildings are becoming more stringent and sophisticated as a result of the quick advancement of science and technology. Due to the limitations of the traditional structural mechanical analysis methods, the calculation results often have large deviations from the actual, and therefore cannot simulate the structural forces and displacements in a more realistic way. The emergence of the finite element method (FEM) makes these complex and irregular problems can be solved well. This paper analyzes the specific applications of FEM and its effectiveness on three typical space structures, namely, space trusses, foundation pits, and steel buildings. The results show that in the analysis of large trusses, the three-dimensional nonlinear finite element analysis using relevant analysis software has good accuracy in displacement calculation, seismic simulation, static force analysis, and structural optimization simulation. In the application of foundation pits, this method can also well simulate the force and deformation characteristics of soil under different working conditions. In steel structure, this method can be applied to steel design, steel slip, and steel top plate force analysis. By discussing the finite element method and related software applications, this paper expects to provide ideas for the analysis of some complex problems in the civil engineering industry and to provide some predictions and suggestions for further advancements.