Introduction: Perforation is the most common complication of sinus floor elevation (SFE) surgery, and is closely associated with the thickness of the maxillary sinus membrane. This study aimed to evaluate the relationship between maxillary sinus membrane thickness and anatomical variations in the osteomeatal complex (OMC). Methods: Cone beam computed tomography scans were retrospectively analyzed, encompassing 1957 sinuses. Mucosal thickness (MT) and mucosal appearance (MA) were classified as normal, flat thickening, polypoid thickening, or ostium obstruction. Ostium width (OW), infundibulum length (IL), and ethmoidal bulla diameter (EBD) were measured. The presence of Haller cells (HC), concha bullosa (CB), and superior attachment of the uncinate process (UPSA) was recorded. Kruskal–Wallis, Mann–Whitney U, Chi-square, and GEE models were used. Results: Mucosal thickening was observed in 54% of the sinuses, with flat thickening (23.5%) being the most prevalent pattern. A significant association was found between ostium obstruction and MT greater than 10 mm. MT, IL, OW, and EBD values were significantly higher in men than in women. Significant correlations were also identified between MT and IL, OW, EBD, and HC. No significant relationship was found between CB and MT. However, UPSA types 3, 4, and 6 were significantly associated with polypoid thickening and ostium obstruction. Conclusion: The findings demonstrate that anatomical variations in the OMC influence maxillary sinus membrane thickness. A comprehensive evaluation of these variations should be performed before planning for SFE procedures. Dentists should be proficient in identifying and assessing the osteomeatal region during routine radiographic examinations to prevent potential complications.