Background: Overlap syndrome (OS), the coexistence of chronic obstructive pulmonary disease and obstructive sleep apnea, is frequently characterized by the presence of daytime hypercapnia (pCO2 ≥ 45 mmHg). The aim of this study was to investigate potential differences in anthropometric, sleep and respiratory characteristics between hypercapnic and normocapnic patients with OS. Methods: Consecutive patients who underwent polysomnography, pulmonary function testing and arterial blood gases and had been diagnosed with OS were enrolled in the study. Results: According to pCO2 levels in wakefulness, the patients were divided into group A, consisting of OS patients without hypercapnia (n = 108) or group B, consisting of OS patients with hypercapnia (n = 55). The majority of included patients in both groups were males (n = 92 in group A vs. n = 50 in group B). Group B had increased BMI (p = 0.001), neck (p = 0.017) and waist circumference (p = 0.013), higher scores in Epworth sleepiness scale (ESS) (p = 0.008), increased sleep efficiency (p = 0.033), oxygen desaturation index (p = 0.004) and time with oxyhemoglobin saturation <90% (p = 0.006) than group A. Also, Group B had decreased average and minimum oxyhemoglobin saturation during sleep (p < 0.001). Hypercapnic patients had lower FEV1% (p = 0.003), FVC% (p = 0.004), pO2 and pCO2 (p < 0.001 for both) values compared with normocapnic patients. In binary regression analysis, which assessed various predictors on the likelihood of having hypercapnia, it was found that BMI (OR: 1.313, 95% CI: 1.048–1.646, p = 0.018) and FVC (OR: 0.913, 95% CI: 0.845–0.986, p = 0.020) were the major determinants of hypercapnia in OS patients. Conclusions: Hypercapnic OS patients were more obese and sleepy and presented worse respiratory function in wakefulness and sleep hypoxia characteristics compared with normocapnic OS patients.