The purpose of this study was to evaluate the effects of segmental osteotomy on the blood vessels and osteoclasts in rats using micro-computed tomography (micro-CT) and histomorphometric analysis. After segmental osteotomy was performed around the maxillary first molars of 36 male Sprague-Dawley rats (n = 72), the samples were divided into a control group (no displacement), 0.5 D group (0.5 mm buccal displacement) and 1.0 D group (1.0 mm buccal displacement) (n = 24/group). At 1, 2, 4 and 8 weeks after surgery, changes in the blood vessel volume were investigated using micro-CT with perfusion of radiopaque silicone rubber. Tartrate-resistant acid phosphatase (TRAP) staining was used for histomorphometric analysis. Two-way repeated measures analysis of variance (rmANOVA) was performed to compare the volume of blood vessels and number of TRAP-positive osteoclasts among the groups. Regarding blood vessel volume, the displacement groups had no significant effects, while the time points had significant effects (p = 0.014). The blood vessel volume at 1 week was significantly smaller than that at 2, 4, and 8 weeks (p = 0.004, p = 0.026, and p = 0.005, respectively). Regarding TRAP cell count, the displacement groups had no significant effects, while the time points had significant effects (p < 0.001). The number of TRAP-positive osteoclasts at 8 weeks was significantly smaller than that at 1, 2, and 4 weeks (p < 0.001, p < 0.001, and p = 0.002, respectively), and the count at 4 weeks was smaller than that at 1 week (p = 0.011). Therefore, a regional osteoclast-related acceleratory phenomenon was maintained until 4 weeks after surgery.