Objective This retrospective study aimed to investigate factors influencing positional changes of the condyle and temporomandibular joint (TMJ) following mandibular defect reconstruction with bone flaps, and to evaluate the biomechanical impacts of flap reconstruction on condylar positioning, thereby providing evidence for optimizing surgical protocols and TMJ functional rehabilitation. Methods A retrospective study was conducted on 90 patients undergoing mandibular segmental resection with immediate bone flap reconstruction at Guizhou Medical University Affiliated Stomatological Hospital (June 2019 to May 2024). After strict screening, 50 cases with complete data were analyzed. Clinical parameters (defect size, location, reconstruction method) and craniofacial CT scans at four timepoints [preoperative (T0), 7-10 days (T1), 3 months (T2), and 6 months (T3) postoperatively] were collected. Mimics 20 software facilitated 3D reconstruction for measuring TMJ anterior/posterior/superior joint spaces (Kamelchuk method) and calculating condylar position via the Pullinger index [Ln (posterior/anterior space)]. Vitral and Krisjane methods quantified mandibular linear parameters (ramus length, condylar pole distances to the sagittal plane, angulation) and glenoid fossa morphology. Statistical analyses were performed using SPSS 21.0. Results Mandibular defect size and location were significant factors influencing postoperative condylar position changes (P<0.05). Compared to preoperative measurements, postoperative condylar anterior, posterior, and superior joint spaces were significantly increased (P<0.001). The most pronounced anterior condylar displacement occurred within 7-10 days postoperatively (P<0.05). In patients with condyle resection, postoperative joint space and angle changes were significant; in patients with condyle preservation, only superior and anterior joint space changes were statistically significant (P<0.05). Additionally, from T1 to T2, the changes in condylar medial-lateral distance, superior joint space, and anterior joint space were negatively correlated with the preoperative condylar position. Compared with preoperative,in the T0-T1 period, condylar medial-lateral distance, posterior joint space, and articular tubercle angle changes were significantly negatively correlated with time (P<0.05). Notably, the angle between the condylar long axis and the coronal axis showed a sustained negative trend from T1 to T3 (P<0.05). Conclusion Condylar position changes after mandibular defect repair with bone flap reconstruction are associated with the size and location of the defect. Additionally, adaptive remodeling of the temporomandibular joint (TMJ) joint space occurs postoperatively. The phenomenon of anterior displacement of the condyle in the early postoperative period (7-10 days) shows a trend of reduction with prolonged follow-up time, and further sample size research is needed.