Obstructive sleep apnea syndrome (OSAS) is one of the most common sleep disorders that endangers human health, which is associated with episodes of apnea or hypopnea during sleep. In children, OSAS is associated with cardiovascular morbidity, neurobehavioral deficits, and poor quality of life, which highlights the importance for early diagnosis and treatment. Recent studies using dynamic magnetic resonance imaging (dMRI) have shown that adults with OSAS exhibit airway narrowing in specific regions that display increased variability in diameter during sleep as compared with controls. In this paper, we propose a novel method to compare OSAS patients with control subjects during awake and asleep states to assess the regional dynamic changes that occur in specific locations of the upper airway. Firstly, we segment the 3D upper airway with a previously developed fully automatic method. Then, different types of breathing cycles are selected by experts based on polysomnography. For each cycle, we calculate the distance of each point on the surface of the upper airway from end-expiration (EE) to end-inspiration (EI), which is then utilized for subsequent motion analysis. The 3D upper airway is subsequently divided into 4 anatomical parts manually. Lastly, comparisons of the dynamic upper airway motion measurements from different cycle groups are performed between OSAS patients and control subjects. Comparisons of different types of cycles within the same anatomical part demonstrated significant differences between control subjects and OSAS patients in all anatomic parts with some exceptions. These novel observations may provide some insights into the pathophysiology of OSAS.