Since the thickness of stacked silicon chips in 3D integration has been thinned to less than 100 μm, the local thermal deformation of the chips has increased drastically because of the decrease of the flexural rigidity of the thinned chips. The clear periodic thermal deformation and thus, the local distribution of thermal residual stress appears in the stacked chips due to the periodic alignment of metallic bumps, and they sometimes deteriorate mechanical and electrical reliability of electronic products. In this paper, the dominant structural factors of the local residual stress in a silicon chip are investigated quantitatively based on the results of a three-dimensional finite element analysis and the measurement of the local residual stress in a chip using stress sensor chips. The piezoresistive strain gauges were embedded in the sensor chips. The length of each gauge was 2 μm, and an unit cell consisted of four gauges with different crystallographic directions. This alignment of the strain gauges enables us to measure the tensor component of three-dimensional stress fields separately. Test flip chip substrates were made of silicon chip on which the area-arrayed tin/copper bumps were electroplated. The width of a bump was fixed at 200 μm, and the bump pitch was varied from 400 μm to 1000 μm. The thickness of the copper bump was about 40 μm and that of tin layer was about 10 μm. This tin layer was used for the formation of rigid joint by alloying it with copper interconnection formed on a stress sensing chip. The measured amplitude of the residual stress increased from about 30 MPa to 250 MPa depending on the combination of materials such as bump, underfill, and interconnections. It was confirmed that both the material constant of underfill and the alignment structure of fine bumps are the dominant factors of the local deformation and stress of a silicon chip mounted on area-arrayed metallic bumps. It was also confirmed that not only the control of mechanical properties of electroplated copper thin films, but also the hound’s-tooth alignment of a through silicon via and a bump are indispensable for minimizing the packaging-induced stress in the three-dimensionally mounted chips. This test chip is very effective for evaluating the packaging-process-induced stress in 3D stacked chips quantitatively.