Objective To compare the effect between computer aided three-dimensional reconstruction of cranial defect cranioplasty and conventional cranioplasty. Methods A total of 84 patients with cranial defects were divided into two groups. One group recevied three-dimensional reconstruction of cranial defect cranioplasty, the other group recevied conventional cranioplasty. Two methods were evaluated through comparing the time of surgery, cosmetic effect and the rate of complications ocurring. Results The group of Three-dimensional reconstruction of cranial defect cranioplasty had shorter moulding time, surgery time and anesthesia time. The differences were statistically significant (t=2.42, 2.70, 2.79,P 0.05).The group of three-dimensional reconstruction of cranial defect cranioplasty had better cosmetic effect; and the patients recovered well without complications such as postoperative infection, blood loss. Conclusions Computer aided three-dimensional reconstruction of cranial defect cranioplasty was more feasible and accurate than conventional cranioplasty.