This paper employs a three-dimensional nonlinear finite element method to analyze settlement and deformation during construction. By considering the interaction between the superstructure, foundation, and subgrade, the method reveals both the magnitude of settlement and the distribution of uneven settlement across the structure. This information is used to adjust the foundation design or implement structural measures to ensure uniform settlement, thereby preventing damage caused by differential settlement. In terms of absolute settlement values, the Mohr-Coulomb model predicts the largest settlement, with a maximum value of approximately 11.7 cm. The linear elastic model calculates the smallest settlement, with a maximum value of around 4.5 cm. The Duncan-Chang model offers an intermediate prediction, with a maximum settlement value of about 8.9 cm. Utilizing the ABAQUS finite element software, a 3D model of a natural foundation strip for a three-story masonry structure was developed. The Duncan-Chang nonlinear elasticity model, which effectively describes the behavior of hardening soil, was applied within the software platform to conduct a detailed numerical simulation. At the same time, the paper assumes that the foundation soil is considered the linear elastic model and the Moore-Coulomb ideal elastic-plastic model is compared with the internal force of the superstructure under different foundation models obtained. According to the maximum principal stress analysis, the areas where the wall may be damaged are received, and the measures to reduce the uneven settlement are proposed.