(1) Background: In this study, the impact of odontogenic risk factors with nasal septum deviation on maxillary sinus mucosal thickening was assessed using Cone-beam computed tomography CBCT. (2) Methods: A total of 328 maxillary sinus regions from 164 patients (85 males and 79 females) were examined. Images were interpreted by dental specialists and Otolaryngologists. Coronal and sagittal sections were examined to assess the proximity of the root tips of posterior maxillary teeth (RPMT) to the maxillary sinus. The periodontal bone loss for all maxillary posterior teeth was also assessed. Consequently, maxillary sinus mucosal thickening (MT) was further classified into three gradings. Multilevel modeling regression analysis was used due to the hierarchical structuring of the data. Four models were developed, a null model with no factors, a model with tooth-level factors (RPMT, PBL, tooth condition, and root length), a model with patient-level factors (gender and nasal septum deviation), and a model with combined patient- and tooth-level factors. Regression estimates (AOR) and 95% confidence intervals (CIs) of individual and tooth factors were calculated. (3) Results: Multilevel regression analysis showed that RPMT was significantly associated with MT of maxillary sinus (p < 0.001), where patients who had RPMT > 0 had higher odds of MT of maxillary sinus. Tooth condition was also found to be significantly associated with MT of maxillary sinus, where teeth with failed RCT (p < 0.001) and teeth with restorations (p < 0.008) had higher odds of MT of maxillary sinus (AOR = 2.87, 95%CI 1.65, 4.42, AOR = 1.64, 95%CI 1.14, 2.36, respectively). (4) Conclusions: In order to plan preoperative treatment for maxillary posterior teeth, it is important to assess the anatomical relationship between the sinus floor and the root tips of the maxillary posterior teeth. Additionally, we establish a better understanding of the clinician before surgical intervention is conducted.