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Objective The study aims to automatically quantify visceral and subcutaneous adipose tissue content using computed tomography (CT) for assessing central obesity severity, and to investigate the impact of central obesity on esophageal motility and mucosal barrier function. Methods This retrospective study included patients who underwent fiberoptic gastroduodenoscopy, high-resolution manometry (HRM), 24-h pH-impedance monitoring, and non-contrast abdominal CT. Participants were stratified into quartiles (Q1–Q4) based on their visceral-to-subcutaneous fat area ratio (V/S), calculated using the TotalSegmentator tool. We compared baseline characteristics, HRM parameters and 24-h pH-impedance parameters across groups. Regression and correlation analyses were performed to evaluate associations between V/S and esophageal motility/mucosal barrier function. Results Of 185 patients stratified by V/S, Group Q1 (V/S ≤ 1.01, n = 48) had mean age 52.75 years and median BMI 24.30 kg/m 2 ; Q2 (1.02 < V/S < 1.29, n = 45): age 56.62 years, BMI 25.95 kg/m 2 ; Q3 (1.30 < V/S < 1.75, n = 46): age 58.43 years, BMI 24.11 kg/m 2 ; Q4 (V/S ≥ 1.76, n = 46): age 60.65 years, BMI 25.67 kg/m 2 . Gastroesophageal reflux disease (GERD) prevalence increased across groups (22.92, 31.11, 34.78, 54.35%). Significant intergroup differences (all P < 0.05) were found in gender, GERD prevalence, lower esophageal sphincter (LES) resting pressure, esophagogastric junction contractile integral (EGJ-CI), acid exposure time (AET), DeMeester score (DMS), and mean nocturnal baseline impedance (MNBI) Z3-Z6. After adjusting for Hiatal Hernia, EGJ type, Mean Acid Clearance Time, and Bolus Clearance Time (BCT) in the linear regression model, V/S was positively correlated with LES resting pressure, EGJ-CI, AET, and DMS, but negatively with MNBI Z3-Z6. Decreased MNBI was primarily associated with acid reflux across all groups, while additional correlations with LES resting pressure and EGJ-CI were observed specifically in groups Q1, Q3, and Q4. The strongest associations were seen in group Q4. Conclusion Central obesity significantly disrupts esophageal motility and weakens the esophageal mucosal barrier, thereby precipitating mucosal injury. Varying degrees of central obesity can further impair the integrity of esophageal mucosa by inducing esophageal motility disorders or acid reflux.