Purpose Many anatomical factors are known to cause obstructive sleep apnea syndrome (OSAS), but only few studies have examined the relationship between the morphology of pterygoid hamulus (PH), upper airway, and OSAS severity. This study aimed to investigate the relationship between the severity of OSAS and PH morphology and other anatomical variations of the upper airway. Methods The data of the patients who underwent polysomnography and diagnosed with OSAS were retrospectively reviewed, and those who underwent paranasal sinus computed tomography were determined. The patients were divided into three groups according to the apnea-hypopnea index (AHI) scores obtained from the polysomnography (mild, moderate, and severe). The relationship between PH thickness, length and interpterygoid distance, and the severity of AHI was investigated. Results Seventy-four patients were included in the study. In patients with severe OSAS (1.83 +/- 0.29 mm), the PH bone thickness was significantly thicker compared to those with mild OSAS (1.59 +/- 0.36 mm) (p = 0.03). When the interpterygoid distance and its ratio to the velopharyngeal length were examined, it was found significantly shorter in patients with severe OSAS than mild cases (p < 0.001; p = 0.045, respectively). Conclusion Our results showed that OSAS severity was associated with hamulus thickness, interpterygoid distance, and the ratio of interpterygoid distance to VL. Our study provides further insight into the pathophysiology of sleep apnea, suggesting that morphometric evaluation of the pterygoid hamulus and upper airway measurements can assist clinicians in stratifying and determining the best treatment options for patients with OSAS.