This study compared the in vivo applicability of three-dimensional uncalcined and unsintered hydroxyapatite/poly-d/l-lactide (3D-HA/PDLLA) with beta-tricalcium phosphate (β-TCP). 3D-HA/PDLLA is a newly developed bioactive, osteoconductive, bioresorbable bone regenerative composite. We performed critical-defect surgery on the mandible body of rats; the defects were filled with one of two bone graft substitutes. After a 4-week follow-up period, the mandibular specimens were examined using hematoxylin and eosin (H&E) staining, immunohistochemistry (IHC) staining and micro-computed tomography (micro-CT). The H&E staining showed an increase in newly formed bone in both groups from week 1 to 4. The difference in the Runx2 IHC optical density (OD) scores of 3D-HA/PDLLA and β-TCP was not statistically significant (p > 0.05); however, the osteocalcin IHC OD scores of the groups differed significantly (p < 0.05). Micro-CT demonstrated a similar trabecular thickness, trabecular spacing, and bone volume per total volume in the two groups (p > 0.05), indicating that bone formation in the two groups was nearly the same from a macro-perspective of bone regeneration. These results demonstrated that a different bone regeneration pattern and earlier osteoblast differentiation occurred in 3D-HA/PDLLA compared with β-TCP. In conclusion, our study demonstrates that 3D-HA/PDLLA is feasible for clinical application as a new bioactive, osteoconductive/bioresorbable bone graft substitute for maxillofacial surgery.