An X-ray micro-tomography system developed in SPring-8 was applied to the evaluation of microstructural evolution ; that is phase growth, appearing as thermal fatigue damage in solder micro-bumps of flip chip interconnects. The obtained CT (Computed Tomography) images show that components of the flip chip such as interconnecting patterns, pads, or bumps are identified with high spatial resolution of about 1μm. Especially, in the the solder bumps, characteristic microstructure is clearly observed, while such information has not been obtained at all by industrially used X-ray CT systems. Remarkable phase growth is also observed clearly as thermal cycle proceeds. This result shows the possibility that nondestructive testing by micro CT system is useful for the evaluation of the thermal fatigue damage in micro-joints.