In Cone Beam Computed Tomography (CBCT) images, accurate tooth segmentation is crucial for oral health, providing essential guidance for dental procedures such as implant placement and difficult tooth extractions (impactions). However, due to the lack of a substantial amount of dental data and the complexity of tooth morphology in CBCT images, the task of tooth segmentation faces significant challenges. This may lead to issues such as overfitting and training instability in existing algorithms, resulting in poor model generalization. Ultimately, this may impact the accuracy of segmentation results and could even provide incorrect diagnostic and treatment information. In response to these challenges, we introduce PPA-SAM, an innovative dual-encoder segmentation network that merges the currently popular Segment Anything Model (SAM) with the 3D medical segmentation network, VNet. Through the use of adapters, we achieve parameter reuse and fine-tuning, enhancing the model’s adaptability to specific CBCT datasets. Simultaneously, we utilize a three-layer convolutional network as both a discriminator and a generator for adversarial training. The PPA-SAM model seamlessly integrates the high-precision segmentation performance of convolutional networks with the outstanding generalization capabilities of SAM models, achieving more accurate and robust three-dimensional tooth segmentation in CBCT images. Evaluation of a small CBCT dataset demonstrates that PPA-SAM outperforms other networks in terms of accuracy and robustness, providing a reliable and efficient solution for three-dimensional tooth segmentation in CBCT images. This research has a positive impact on the management of dentofacial conditions from oral implantology to orthognathic surgery, offering dependable technological support for future oral diagnostics and treatment planning.