The aim of this study was to investigate the influence of ultrasonic surgical method (piezoelectric surgery) on invasions of bone structure in early stages and the subsequent healing process of bone defects of rat calvaria as compared with that of rotary cutting using an appropriate rotation speed. Thirteen-week-old male Sprague-Dawley rats were used in this study. Bone defects were prepared in rat calvaria using either an ultrasonic surgical instrument with an ultrasonic insert tip (Ui) or a handpiece with a round bur (Rb) as a rotary cutting instrument (control). Morphological evaluations of the cutting surfaces in the bone defects were assessed by scanning electron microscope (SEM) and confocal laser microscope (CLM) observation. The degree of invasions of the bone structure in the early stages after bone defects were made was assessed by the ratio of empty osteocyte lacunae relative to the total number of osteocytes. The process of bone healing was analyzed by histological observation, immunohistochemical staining with proliferating cell nuclear antigen (PCNA) and osteocalcin (OC), and ratio of PCNA-positive cells. Many fine, parallel streaky cutting traces were observed in the Ui groove surfaces, whereas the Rb groove surfaces were flat and no parallel cutting traces were observed. The arithmetic average roughness of the Ui group (10.06 ± 1.96 µm) was significantly higher than that of the Rb group (2.52 ± 0.16 µm) (p < 0.05). During the entire observation period, no differences in histological observation and immunohistochemical staining were observed between the Ui and Rb groups. No significant differences were recognized in the ratio of empty lacunae and PCNA-positive cells between the Ui and Rb groups. In the present study, there were no appreciable differences in the invasions of bone structure in the early stages and the subsequent healing process of the bone defects of rat calvaria between ultrasonic surgical method and rotary cutting method.