The bottom-frame structure is a kind of small bay masonry structure building with large bay RC frame in bottom, it is widely exists near streets in China because of the economy and applicability. But for the poor correspondence capacity for foundation’s deformation, it is easily be damaged for this kind of building in uneven settlement. It can provides theoretical support for design and strengthening works of such kind of structure buildings by analyzing the relation between superstructure’s stiffness and settlement of foundations, which has practical significance. For the complexity of stress of the composite structure, ANSYS is used in this analysis. A strengthening project based on this theory is introduced in the end, it validates the feasibility of the conclusion.