Objectives: This study aimed to develop and validate a hybrid deep learning model combining Convolutional Neural Networks (CNN) and Vision Transformers (ViT) to automatically classify maxillary sinus membrane morphologies on Cone-Beam Computed Tomography (CBCT) images, distinguishing between Normal, Flat, Polypoid, and Obstruction types. Methods: A dataset of 959 CBCT images was collected and categorized into four morphological classes: Normal, Flat, Polypoid and Obstruction. A custom hybrid model was developed, integrating a lightweight residual CNN for local feature extraction, learnable weighted feature fusion with a bidirectional feature pyramid network and a Transformer encoder for global context modeling. The performance of proposed model was compared against six different architectures, including ResNet50, MobileNetV3L and standard ViT models, using accuracy, precision, recall and F1-score metrics. Results: The proposed hybrid model achieved the highest overall accuracy of 98.44%, outperforming six strong CNN and ViT models including ResNet50 (97.92%) and ViT-B16 (86.46%) models. In class-wise analysis, the model demonstrated superior diagnostic capability, particularly for the “Obstruction” class, achieving 100% accuracy. High discrimination was also observed for “Flat” (98.21%) and “Polypoid” (98.04%) morphologies, confirming the model’s sensitivity to shape-based features. Conclusions: The proposed hybrid CNN-ViT model successfully classifies maxillary sinus membrane morphologies with high accuracy, effectively overcoming the limitations of standard ViT models on limited datasets. Detection of membrane morphology is vital for predicting surgical risks like membrane perforation and post-operative sinusitis. This model serves as a reliable clinical decision support tool, enabling clinicians to objectively assess specific risk factors before implant surgery and sinus floor elevation.