This study aimed to investigate the accuracy and safety of mandibular osteotomy and distraction device positioning in distraction osteogenesis assisted by an electromagnetic navigation surgical robot. Twelve New Zealand white rabbits were randomly divided into two groups after computed tomography. The control group underwent a procedure based on the preoperative three-dimensional design and clinical experience. Animals in experimental group underwent a procedure with robotic assistance after registration. The accuracies of osteotomy and distraction device positioning were analysed based on distance and angular errors. The change in ramus length after a 1 cm-extension of the distraction device was for assessing distraction effect. The preparation, operative and osteotomy times, intraoperative bleeding, and teeth injury were used for safety assessment. In the experimental group, the distance (t = 2.591, p = 0.011) and angular (t = 4.276, p = 0.002) errors of osteotomy plane, and the errors in distraction device position (t = 3.222, p = 0.009) and direction (t = 4.697, p = 0.001) were lower; the distraction effect was better (t = 4.096, p = 0.002). There was no significant difference in the osteotomy time and bleeding; however, the overall operative and preparation times were increased in the experimental group, with a reduced rate of teeth damage. Robot-assisted mandibular distraction osteogenesis with electromagnetic navigation in craniofacial microsomia is feasible, safe, significantly improves surgical precision.