Prosthesis for missing maxillary molars with dental implants often requires maxillary sinus augmentation owing to insufficient alveolar bone height. However, the anatomical structure of the maxillary sinus is a significant risk factor. This study used preoperative cone-beam computed tomography (CBCT) to investigate changes in the anatomical structure of the maxillary sinus due to tooth loss and conducted an epidemiological survey of Japanese people to determine the effects of gender and age on these changes. Preoperative CBCT scans were analyzed in patients aged ≥ 50 years with free-end maxillary molar edentulism involving ≥ 2 missing teeth seeking implant treatment. Statistical analyses were performed. One hundred and twenty participants (46 males, 74 females; mean age, 62.1 ± 7.4 years) with 3.0 ± 0.9 missing teeth and an existing bone volume of 6.2 ± 3.1 mm were included. Lateral wall thickness, sinus angle, sinus membrane thickness, maxillary sinus length and width, and the presence of the sinus septa significantly differed between missing and non-missing sides. Maxillary sinus height and sinus membrane thickness on missing side and maxillary sinus height and width on non-missing side varied significantly. Aging was associated with maxillary sinus length and width changes on the non-missing side in males, whereas no age-associated effects were identified in females. To ensure the safe execution of maxillary sinus augmentation, a thorough understanding of maxillary sinus anatomy is crucial prior to surgery.