Body fat indices serve as predictive markers of insulin resistance (IR) in metabolic diseases. IR is common in obstructive sleep apnea (OSA). However, whether body fat indices have utility as predictors of IR in OSA remain unknown. A longitudinal study was conducted in 46 patients undergoing bariatric surgery to explore the relationship between IR and body fat indices. Then, a cross-sectional study was performed to evaluate the relationships between body fat indices and IR, and receiver operating characteristic (ROC) curves were generated. Body indices, homeostasis model assessment index of insulin resistance (HOMA-IR), biological indicators, and polysomnographic variables were collected. In the longitudinal study, significant relationships were found between remission of IR and changes in visceral adiposity index (VAI) (r = 0.452, P < 0.05) and triglyceride-glucose index (TyG) (r = 0.650, P < 0.01). In the cross-sectional study, lipid accumulation product (LAP) (best cutoff value: 30.16, area under the curve (AUC) = 0.728, P < 0.001) and TyG (best cutoff value: 8.54, AUC = 0.740, P < 0.001) were indicators of IR in normal weight group. In overweight/obese group, body mass index (BMI) (best cutoff value: 27.69 AUC = 0.707, P < 0.001) and waist circumference (WC) (best cutoff value: 97.25, AUC = 0.708, P < 0.001) were markers of IR. TyG showed better ability to predict IR in normal weight females (best cutoff value: 8.39 AUC = 0.813, P < 0.001). Body fat indices are predictive markers of IR in patients with OSA.