To investigate bone remodelling responses to mandibulectomy, a joint external and internal remodelling algorithm is developed here by incorporating patient-specific longitudinal data. The primary aim of this study is to simulate bone remodelling activity in the conjunction region with a fibula free flap (FFF) reconstruction by correlating with a 28-month clinical follow-up. The secondary goal of this study is to compare the long-term outcomes of different designs of fixation plate with specific screw positioning. The results indicated that the overall bone density decreased over time, except for the Docking Site (namely DS1, a region of interest in mandibular symphysis with the conjunction of the bone union), in which the decrease of bone density ceased later and was followed by bone apposition. A negligible influence on bone remodeling outcome was found for different screw positioning. This study is believed to be the first of its kind for computationally simulating the bone turn-over process after FFF maxillofacial reconstruction by correlating with patient-specific follow-up.