Objective: This study aimed to examine the morphological characteristics of the nasopharynx in unilateral Cleft lip/palate (CL/P) children and non-cleft children using cone beam computed tomography (CBCT). Methods: A retrospective study consisted of 54 patients, of which 27 patients were unilateral CL/P, remaining 27 patients have no CL/P. Eustachian tubes orifice (ET), Rosenmuller fossa (RF) depth, presence of pharyngeal bursa (PB), the distance of posterior nasal spine (PNS)-pharynx posterior wall were quantitatively evaluated. Results: The main effect of the CL/P groups was found to be effective on RF depth-right (p < 0.001) and RF depth-left (p < 0.001). The interaction effect of gender and CL/P groups was not influential on measurements. The cleft-side main effect was found to be effective on RF depth-left (p < 0.001) and RF depth-right (p = 0002). There was no statistically significant relationship between CL/P groups and the presence of bursa pharyngea. Conclusions: Because it is the most common site of nasopharyngeal carcinoma (NPC), the anatomy of the nasopharynx should be well known in the early diagnosis of NPC.