Animal models were widely used in the research of the etiology, pathogenesis, prevention, treatment of human diseases, and the development of new animal models of human diseases could greatly promote relevant research progress. In this study, a new bone defect model based on zebrafish was explored. Optical coherence tomography (OCT) was used to evaluate the building and repairing process of bone defect model in vivo. Thirteen adult zebrafish of the same size were used in this study, of which 10 were molded with bone defects and the remaining 3 were used as control. Firstly, each zebrafish skull was scanned by OCT, and then a hole about 200 microns in diameter was opened in the optic parietal region of the skull with a self-developed tool to form a bone defect. OCT was used to evaluate the skull injury of each zebrafish on the 2nd, 5th, 9th, 11th, 14th and 21st day, respectively. Twenty-one days after recovery, pathological experiments were performed to evaluate zebrafish skull. The pathological results of the defected skull were compared with OCT results. The experimental results showed that OCT could evaluate the process of bone defect recovery in vivo with high resolution. The new bone is clearly visible. The results of OCT imaging were highly matched with those of pathological results. In conclusion, the strategy of combining zebrafish model with OCT imaging technology will provide new impetus for the study of bone defect diseases.