<p>Many applied materials are cooled from high temperatures to a suitable temperature; however, their physical properties may be affected by different cooling conditions. In this study, a numerical simulation of the physical changes in multiphase materials during cooling was conducted. A three-dimensional physical model based on a typical multiphase material with a core-bonding structure synthesized from calcium, silicon, and iron oxides was constructed by serial sectioning technology. Next, to study the temperature and stress distribution of such materials under different cooling conditions and at different times, the Biot number (<i>Bi</i>) and Fourier number (<i>Fo</i>) were introduced. Furthermore, transient coupled thermomechanical calculations were performed to elucidate the mechanism of crack initiation. During cooling, the simulation results suggested that the temperature distribution of the material is affected mainly by geometric factors instead of the phase composition and that the rate of decrease in the temperature near the holes increases significantly. With respect to the stress distribution, the distribution of the maximum principal stress is affected mainly by the physical properties of the phase, and the stress gradient is concentrated at the interface of the phases, especially along the boundary between the bonding and core phases. In addition, the results revealed that the surface unit experienced the highest von Mises stress, followed by the radial midpoint unit and the center unit. Sensitivity analysis revealed that even with a 40% reduction in the elastic modulus or a 10% increase in the thermal expansion coefficient, the relative stress ranking (surface &gt; radial midpoint &gt; center) remained unchanged. These findings provide quantitative guidance for optimizing cooling process, particularly when slower initial cooling (800–500&#xa0;°C) is recommended to reduce thermal gradients at the surface.</p>