For the first time, finite element analysis (FEA) is applied to the thermal-compression flip-chip process in microelectronics. By adding the bump height non-uniformity and the morphology variance, a common basal line is established. Although the experiment confirms the rate-dependence of indium, an approximation is made to derive the material properties in FEA. The relative standard deviation (RSD) of deformation between the FEA model and the reality is around 1% when predicting the misaligned flip-chip specimen. Besides, the modeled bump characteristic with misalignment coincides with the cross-sectional scanning electron microscope (SEM) picture. The model could be served as a powerful tool to guide the manufacturing process.