In reconstructive surgery following partial mandibulectomy, the biomechanical integrity of the fibula free flap applied to the remaining mandibular region directly influences the prognosis of the surgery. The purpose of this study is to evaluate the biomechanical integrity of two fixation materials [titanium (Ti) and hydroxyapatite/poly-L-lactide (HA-PLLA)]. In this study, we simulated the mechanical properties of miniplate and screw fixations in two different systems by finite element analysis. A three-dimensional mandibular model was constructed and a fibula free flap and reconstruction surface were designed. The anterior and posterior end of the free flap was positioned with two miniplates and two additional miniplates were applied to the angled area of the fibula. The masticatory loading was applied considering seven principal muscles. The peak von Mises stress (PVMS) distribution, size of fixation deformation, principal stresses on bones, and gap opening size were measured to evaluate the material properties of the fixation. In the evaluation of properties, superior results were observed with both fixation methods immediately after surgery. However, after the formation of callus between bone segments at 2 months, the performance of Ti fixation decreased over time and the differences between the two fixations became minimal by 6 months after surgery. The result of the study implies the positive clinical potential of the HA-PLLA fixation system applied in fibula free flap reconstruction.