In this study, the bone regeneration efficacy of dehydrothermally (DHT) cross-linked collagen membrane with or without a bone graft (BG) material was evaluated in a critical-sized rat model. An 8-mm-diameter defect was created in the calvaria of 40 rats, which were randomized into four groups: (1) control; (2) DHT; (3) BG; and, (4) DHT + BG. Evaluations were made at 2 and 8 weeks after surgery using micro-computed tomographic (micro-CT), histological, and histomorphometric analyses. Micro-CT analysis showed an increase in the new bone volume (NBV) of the BG and DHT + BG groups at 2 weeks after surgery, representing a significant difference (p < 0.05). At 8 weeks after surgery, the NBV increased in all four groups. However, larger NBVs were observed in the BG and DHT + BG groups, and a significant difference was no longer observed between the two groups. Histologic analysis demonstrated that the graft materials sustained the center of the defect in the BG and DHT + BG groups, which was shown in histomorphometric analysis as well. These results suggest that DHT membrane is a safe biomaterial with adequate tissue integration, and has a positive effect on new bone formation. Moreover, the best effects were achieved when DHT was used in conjunction with BG materials.