This retrospective comparative cohort study assessed whether maxilla-first versus mandible-first sequencing affects postoperative TMD outcomes. Consecutive patients undergoing bimaxillary orthognathic surgery between 1998 and 2025 were included when standardized preoperative and postoperative temporomandibular joint assessments were available. TMD evaluation comprised Research Diagnostic Criteria for Temporomandibular Disorders diagnoses, as well as Helkimo Anamnestic (Ai) and Clinical Dysfunction (Di) indices. Primary outcomes included postoperative disc displacement (DD) and myofascial pain dysfunction (MPD), whereas secondary outcomes were postoperative Ai and Di severity. Descriptive, bivariate, and multiple logistic regression analyses were performed, with statistical significance set at P ≤ 0.05. A total of 292 patients were included, of whom 153 underwent maxilla-first and 139 mandible-first surgery. Surgical sequencing was not independently associated with postoperative DD, MPD, Ai, or Di outcomes. In contrast, baseline TMD status emerged as the strongest predictor of postoperative dysfunction. Preoperative DD independently predicted postoperative DD (OR, 3.01; P < 0.001), whereas preoperative MPD independently predicted postoperative MPD (OR, 5.13; P < 0.001). Increasing age and female sex were also associated with greater postoperative symptom severity. These findings suggest that postoperative TMD outcomes are primarily driven by baseline TMD severity and patient-related factors rather than by the intraoperative osteotomy sequence.