Ultrasonic osteotomy devices (UODs) have emerged as precise bone-cutting instruments with soft tissue-sparing benefits; yet their impact on bone healing and adjacent neural tissue remains underexplored. This study aimed to investigate the effects of UODs versus conventional rotary high-speed burr (HSB) on bone healing and central nervous functions using mouse split calvarial bone defect models. Bilateral parietal bone defects were created in the skulls of mice using UOD (right) and HSB (left). Intraoperative heat generation was recorded using a thermal camera. Bone healing progress was assessed via longitudinal micro-CT over 8 weeks, supplemented by histological (H&E staining) and neurofunctional (cylinder test) analyses at 2-, 4-, 6-, and 8-week intervals. All 24 mice completed the 8-week follow-up without complications. Micro-CT revealed comparable bone defect closure rates between groups (p > 0.05). Despite irrigation, UOD generated transient temperature spikes exceeding 60 °C. Histologically, UOD-treated bone adjacent to defects displayed loosened, wave-like multilayered structures. UOD sides also showed brain tissue hyalinization and structural defects, correlating with transient parietal lobe dysfunction in cylinder tests. UOD induced transient thermal spikes, altered bone morphology, and subtle neurofunctional changes. Caution is advised when deploying UODs near neural tissues or delicate bone regions.