Obesity is strongly correlated with the pathogenesis of obstructive sleep apnea (OSA); myokines may play important roles in this condition. We performed a body mass index- (BMI) and physical activity- (PA) matched study to explore the relationship between the irisin level and OSA. Ninety-six consecutive participants were recruited. After matching in terms of BMI and PA, 28 OSA patients and 28 healthy controls were finally included. Whole-night laboratory-based polysomnography was used to identify OSA. The Recent Physical Activity Questionnaire and Epworth Sleepiness Scale Questionnaire were employed to assess PA over the past 4 weeks, and daytime sleepiness. We measured serum irisin, fasting blood glucose, and insulin levels in blood samples. The serum irisin concentrations differed significantly between the control, mild OSA, moderate OSA, and severe OSA groups (p < 0.001) and correlated significantly with the apnea/hypopnea index (AHI) (r = -0.787, p < 0.001). All of age, BMI, neck, waist and hip circumferences, fasting blood glucose level, and the Epworth Sleepiness Scale and PA scores were associated with irisin levels (p < 0.05). After adjustment for these factors, the serum irisin level was independently correlated with the AHI (r = -0.428, p = 0.002). On forward logistic regression analysis, the association remained significant in the final multiple regression model (β = -0.107, p < 0.001). The serum irisin concentration was significantly correlated with OSA severity, independently of BMI and PA. Further studies are needed to determine the molecular mechanisms in play.