BackgroundAssessing condyle position post orthognathic surgery is pivotal for optimizing surgical accuracy, sustaining postoperative stability, and ensuring predictable treatment outcomes. PurposeThe aim of this study was to analyze the changes of condyle position after orthognathic surgery with different types of jaw deformity and to analyze whether the changes of condyle position are different. Study design, setting, sampleA retrospective cohort study was designed and conducted, involving adults who underwent orthognathic surgery for jaw deformities at the affiliated Stomatological Hospital of Nanchang University between 2019 and 2022. Patients with incomplete CT data were excluded. Predictor/exposure/independent variableThe primary predictor variable was time (pre-operative and post-operative) and types of jaw deformities (skeletal Class III, skeletal Class II, and mandibular deviation). Main outcome variable(s)The main outcome variables were the 3D linear and rotational positional changes of the condyle. CovariatesEvaluated covariates included sex and age. AnalysesMIMICS 20.0 software measured all data, and SPSS 22.0 software facilitated statistical analyses. Intra- and inter-group correlation analyses employed paired t-tests and independent t-tests, with statistical significance set at P < 0.05. ResultsThe study sample was composed of 32 subjects with a mean age of 22.43±1.6 and 9 were male. The analysis of changes of condylar position from virtual surgical planning to immediate postoperative period showed that the maximum condylar displacement was 1.74 mm and the maximum angular change was 3.92°. The analysis of changes in condylar position from the immediate postoperative period to 1-year postoperatively showed no statistically significant changes for the same type of jaw deformity. But patients with Class II malocclusion exhibited distinct condylar displacement and rotation patterns compared to those with Class III malocclusion and mandibular deformity. Conclusions and RelevanceThe application of virtual surgical planning in orthognathic surgery ensures a high degree of consistency in achieving the desired condylar position. Moreover, no significant change in condylar position was observed after orthognathic surgery for the same type of jaw deformity. However, patients with Class II deformities exhibited a higher susceptibility to rotational displacement of the condyles compared to those with other types of jaw deformities.