Purpose <p>To investigate the relationship between obstructive sleep apnea hypopnea syndrome (OSAHS) severity and fat, bone, and muscle indices.</p> Methods <p>This study included 102 patients with OSAHS and retrospectively reviewed their physical examination data. All patients underwent polysomnography, body composition analysis, dual-energy X-ray absorptiometry, computed tomography (CT) and blood test. Correlation and multiple linear regression analyses were performed using SPSS 22.0.</p> Results <p>Among the fat indices, fat mass (FM) (<i>r</i> = 0.27–0.43), body fat percentage (BFP) (<i>r</i> = 0. 25–0.35), visceral fat area (VFA) (<i>r</i> = 0.28–0.40) and trunk fat mass (TFM) (<i>r</i> = 0.26–0.34) were positively correlated with hypopnea index (HI), apnea-hypopnea index (AHI), oxygen desaturation index (ODI), and percent of time spent with oxygen saturation below 90% (T90%), respectively, and negatively correlated with mean pulse oxygen saturation (SpO₂) (<i>r</i>= -0.28–-0.41). For bone indexes, T8, T9, T11, L1-CT value, mean vertebral CT value and 25-Hydroxyvitamin D3 were positively correlated with mean SpO₂ (<i>r</i> = 0.23–0.32), respectively. For muscle indexes, pectoralis muscle density (PMD) was negatively correlated with HI, AHI, and ODI (<i>r</i>= -0.20–-0.36) and positively correlated with mean SpO₂ (<i>r</i> = 0.26). In separate models predicting sleep measures, AHI increased by 0.36, 0.29, 0.34 and 0.25 events/h per unit increase in FM, BFP, VFA, and triglyceride (TG), respectively. AHI decreased by 0.27 per unit increase in PMD. T90% increased with FM, BFP, VFA, WHR, TG and total cholesterol (TC), but decreased with appendicular skeletal muscle mass (ASM) and PMD respectively.</p> Conclusion <p>Higher fat levels and lower vertebral CT values, muscle mass and density correlated with a higher degree of OSAHS severity. Intermittent hypoxia may affect fat, bone, and muscle metabolism in patients with OSAHS.</p>