Phase-contrast X-ray computed tomography (CT) is a unique technique for the observation of phase changes of compounds due to its high sensitivity to density. Owing to the difficulty in controlling the temperatures of samples without disrupting the measurement of the X-ray phase-shift, the application of the X-ray CT, except under room temperature conditions, has been limited. We have developed a temperature-controlled system for the X-ray CT measurements. In this report, nondestructive three-dimensional (3D) observations under different temperature conditions using phase-contrast X-ray CT techniques are presented. These techniques allow the visualization of temperature-controlled crystals composed of water molecules and their growth in complex materials.