There is plenty of literature on masticatory function and its impact on maxillofacial development. However, the influence of masticatory hypofunction on bone turnover in the alveolar bone has hardly been studied. This study aimed to clarify the influence of tooth loss and soft diet on the alveolar bone turnover during the growth period. Three-week-old Wistar rats were randomly divided into the following three groups: Hard diet group (rats raised on solid standard diet), Powder diet group (rats raised on powdered standard feed diet), and Extraction group (rats raised on powdered standard diet with maxillary molars extraction). BV, BMC, and BMD in the cancellous bone of M1 were measured using micro-CT analysis. To analyze the histological bone turnover, we prepared non-decalcified thin sections of alveolar cancellous bone when rats were 20 weeks old. On three-dimensional constructed images, the experimental groups (the Powder diet and Extraction groups) showed expansion of the medullary cavity of the interradicular septum of the first molar compared to controls (the Hard diet group). BV, BMC, and BMD were significantly lower in the experimental groups, with the difference from controls being greater in the Extraction group. On histomorphometric analysis, the bone mass parameters, bone formation parameters, and bone mineralization parameters were significantly lower in the experimental groups compared to controls. The bone resorption parameters were significantly higher in the experimental groups. From this study, we found that soft diet and tooth loss might worsen the bone microstructure, reduce osteogenesis, and promote bone resorption in alveolar bone.