Recent excavation of the elephant ivories at the Sanxingdui site of the Shang Dynasty in Sichuan, China brings attention to the burnt features of the ivories. However, burnt ivories cannot be assessed by the same criteria established for burnt bones because of the differences in the ways that the two materials respond to heat. This study examines differences in the phase transition characteristics of ivory and bone, and confirms that the threshold temperature of the alteration in ivories is lower than that in bones. In our analysis, elephant ivories and bovine bones burnt at the temperatures between 200 and 1000 °C in oxidizing or reducing atmosphere are prepared and comparatively investigated by attenuated total reflection Fourier transform infrared spectroscopy. The results show that the transformation from magnesium-substituted hydroxyapatite (Mg-HAp) to magnesium-substituted β-tricalcium phosphate in ivory dentin takes place at the temperature as low as 800 °C, while β-tricalcium phosphate is not observed in bovine bones burnt at 1000 °C or below mainly because of the different magnesium contents. Due to the destruction of Mg-HAp at 800 °C in ivories, cyanamidapatite that could form in bones burnt under reducing atmosphere is absent in burnt ivories. With reference to the experimental burnt ivories, archaeological burnt ivories from the Sanxingdui site can now be clearly determined to be burnt unevenly at temperatures up to around 800 °C. This study may provide further information for archaeological research on ivories from the Sanxingdui site and identification of burnt bioapatite materials in other archaeological findings.