Objective <p>PXseg, a novel approach for tooth segmentation, numbering and abnormal morphology detection in panoramic X-ray (PX), was designed and promoted through optimizing annotation and applying pre-training.</p> Methods <p>Derived from multicenter, ctPXs generated from cone beam computed tomography (CBCT) with accurate 3D labels were utilized for pre-training, while conventional PXs (cPXs) with 2D labels were input for training. Visual and statistical analyses were conducted using the internal dataset to assess segmentation and numbering performances of PXseg and compared with the model without ctPX pre-training, while the accuracy of PXseg detecting abnormal teeth was evaluated using the external dataset consisting of cPXs with complex dental diseases. Besides, a diagnostic testing was performed to contrast diagnostic efficiency with and without PXseg’s assistance.</p> Results <p>The DSC and F1-score of PXseg in tooth segmentation reached 0.882 and 0.902, which increased by 4.6% and 4.0% compared to the model without pre-training. For tooth numbering, the F1-score of PXseg reached 0.943 and increased by 2.2%. Based on the promotion in segmentation, the accuracy of abnormal tooth morphology detection exceeded 0.957 and was 4.3% higher. A website was constructed to assist in PX interpretation, and the diagnostic efficiency was greatly enhanced with the assistance of PXseg.</p> Conclusions <p>The application of accurate labels in ctPX increased the pre-training weight of PXseg and improved the training effect, achieving promotions in tooth segmentation, numbering and abnormal morphology detection. Rapid and accurate results provided by PXseg streamlined the workflow of PX diagnosis, possessing significant clinical application prospect.</p>