Purpose: This study compared modified distraction osteogenesis (DO) protocol with conventional DO protocol on healing bone formation. Computer simulation was performed to understand the mechanical environment of modified DO protocol, which applies compression during the consolidation period. Materials and Methods: Fifty rats were used in this study. Twenty-five rats in the conventional DO (control) group were sacrificed at postoperative days 11, 21, 28, 35, and 49 after osteotomy. In the modified DO (experimental) group, compression was applied on day 7 after distraction (day 18 postoperatively) for 4 days during the early consolidation period and 25 rats were sacrificed on postoperative day 19, 28, 39, 46, and 53. The histologic and radiographic findings were used to compare the 2 groups. Further, computer simulation was used to predict the mechanical environment of healing bone under conventional and modified DO protocol. Results: Radiographic findings showed that the experimental group resulted in denser and wider healing bone. Histologically, the experimental group yielded more mature lamellar bone than the control group. Computer simulation showed that absolute values of tissue strains were nearly double in the control group because of the softer healing tissues. Both the experimental and control groups showed high strains at the ridge crest. Concentrated tensile strain along the distraction direction at the ridge crest might hinder bone formation at the interface, while compressive strain could facilitate the process. Conclusion: This study proposed a modified DO protocol of adding compression during the early consolidation period of conventional DO protocol. This new technique appears to provide faster and denser bone regeneration.