There have been numerous reports on the effects of the reduced masticatory function on jawbone growth, but the types of changes that occur during each period remain unclear. The objective of this study was to elucidate the effects of the reduced masticatory function on the jawbone over time. Micro-computed tomography (micro-CT) was used to scan the heads of rats that underwent extraction of all maxillary molars at the age of 5 weeks and were reared on a powdered diet, and the heads of control rats that did not undergo molar extraction and were reared on a solid diet. The changes in jawbone morphology up to 20 weeks were investigated in both groups. There were no significant differences in the maxillary or mandibular size, but the mandibular ramus length was significantly smaller in the extraction group from 9 weeks to 20 weeks, while the mandibular angle was significantly larger from 7 weeks to 20 weeks. The mandibular area was also significantly smaller from 7 weeks to 20 weeks, the area of the mandibular notch was significantly larger from 7 weeks to 20 weeks, and the mandibular thickness was significantly smaller from 9 weeks to 20 weeks. These results suggest that the reduced masticatory function affects mandibular growth and development from 2-4 weeks after molar extraction.