Thermal management is a key technology to desterilize unused energy sources for building sustainable societies. However, conventional temperature measurement methods such as infrared thermography can detect only the surface temperature of objects because they use infrared light. We thus present a novel three-dimensional X-ray thermography using a phase-contrast X-ray imaging technique, which enables non-destructive observations of the inner thermal distribution of samples. The sensitivity of phase-contrast X-ray imaging is about 1000 times higher than that of conventional X-ray imaging. Therefore, temperature changes can be detected by using density changes caused by thermal expansion. We applied X-ray interferometric imaging (XI) that detects phase-shift by using a crystal X-ray interferometer. The highest sensitivity of XI was utilized to successfully obtain the first three-dimensional image that visualizes the thermal distribution in heated water nondestructively. Additionally, projection images visualizing the dynamic thermal flow in heated water were also obtained, and their distribution and diffusion velocity agreed well with those of the calculated images obtained by computational fluid dynamics analysis. These results show that the novel thermography enables nondestructive observations of inner temperature and thermal flow and can provide solutions for optimum thermal design of electrical devices, motors, and engines.