Objective This study aimed to assess the association between thickening of mucosa of floor of maxillary sinus and the anatomical structure of edentulous region by cone beam CT (CBCT), offering important information for maxillary sinus lift and dental implant treatment. Methods The cone beam CT images taken at the Department of Periodontics in the Stomatological Hospital of Tianjin Medical University and Guangzhou Medical University from January 2013 to May 2022 were used for measurement. A total of 103 patients met the inclusion criteria for evaluation thickening of mucosa of floor of maxillary sinus (＞2mm) On the CBCT images, the alveolar bone height and width, the distance from the lateral wall blood vessels to floor of maxillary sinus, together with the anterolateral thickening of maxillary sinus to study the influence of thickening of mucosa of floor of maxillary sinus on the anatomical structure of edentulous region. Results There were 56 patients in the maxillary sinus floor mucosal thickening group and 47 patients in the non-maxillary sinus floor mucosal thickening group. The study showed that the maxillary sinus floor mucosal thickening group had larger height of alveolar bone than the non-maxillary sinus floor mucosal thickening group (P＝0.0246) However, no statistically significant differences were observed in the alveolar bone width (P=0.1184), the anterolateral thickening of maxillary sinus (P=0.907) and the lateral wall blood vessels to floor of maxillary sinus (P=0.4718) Conclusion From the result of this study, it can be concluded that there is an association between increasing maxillary sinus mucosal thickening and changes in alveolar bone height after tooth extraction