The 3D numerical analysis is carried out to investigate the settlement behavior of flexible mat foundations subjected to vertical loads. Special attention is given to the improved analytical method (YS-MAT) that reflects the mat flexibility and soil spring coupling effect. The soil model captures the stiffness of the soil springs as well as the shear interaction between the soil springs. The proposed method has been validated by comparing the results with other numerical methods and a field measurement on mat foundation. Through comparative studies, the settlement of the proposed method was in relatively good agreement with those of a field measurement and other numerical methods. The results permit us to estimate the response of the mat foundation subjected to vertical loads that should be taken into account in the combination of mat flexibility and soil continuity characteristics.