New nondestructive inspection methods with high spatial resolution are expected to support the evaluation and enhancement of the reliability of microjoints on printed circuit boards. An X-ray microtomography system, the SP-μCT has been developed at the Super Photon ring-8 GeV (SPring-8), the largest synchrotron radiation facility in Japan. In this work, the SP-μCT was first applied to the nondestructive evaluation of thermal fatigue phenomena, namely microstructure evolution (i.e., phase growth) and microcrack propagation, appearing in actual solder microbumps of flip chip interconnects due to thermal cyclic loading. In addition, a refraction-contrast imaging technique was simultaneously applied to visualize the fatigue cracks with an actual opening of less than 100 nm. The observed specimen has a flip chip structure joined by Sn-37wt%Pb eutectic solder bumps 150 μm in diameter. Consequently, the process of phase growth and crack propagation was determined via observation of consecutive computed tomography (CT) images obtained in the same plane of the same specimen. As the thermal cycle proceeded, remarkable phase growth was clearly observed, followed by the appearance of fatigue cracks in the corners of the interfaces between the solder bump and Cu pad. Moreover, the CT images also enabled us to evaluate the fatigue lifetime of the bumps, as follows. The lifetime to fatigue crack initiation was estimated by quantifying the increase in the phase growth. The crack propagation lifetime to failure was then determined by measuring the average crack propagation rate. Such results have not been obtainable at all by X-ray CT systems for industrial use and demonstrate the possibility of nondestructive inspection by a synchrotron radiation X-ray microtomography system.