Due to high performance demand, the dimensions of chips should be reduced so the stacked 3D-ICs are introduced into semiconductor industry. For small substrate dimensions and high interconnects requirements, the FR-4 substrates are substituted by the Si substrates. The Si chips and substrates are thinned down. A rigid material like Si suffers much larger thermal stress when the thickness is below 100 micron. The reliability issues would be a serious concern in high temperature applications. In this study, the z-axis strain in the thin Si chip caused by the thermal expansion mismatch between Si and underfill was in-situ measured at different temperature by utilizing the synchrotron radiation X-ray diffraction method. The value was 1-ordered larger than the thick Si chips. The stress values would be similar to the stress values that were measured from the flip chip with FR-4 substrates. These results show that the stress issue is critical in the stacked IC chips. The in-situ synchrotron radiation X-ray has the characteristics of high intensity, high precision, and high collimation. Therefore, the stresses distribution on the Si chip could also be precisely measured. The results show that the center of silicon chips would suffer the largest stress and the variations of stress state at different temperatures also reveal that the underfill plays an important role even if the substrates are substituted by silicon.