MOTIVATION: Post-translational modification (PTM) crosstalk events play critical roles in biological processes. Several machine learning methods have been developed to identify PTM crosstalk within proteins, but the accuracy is still far from satisfactory. Recent breakthroughs in deep learning and protein structure prediction could provide a potential solution to this issue. RESULTS: We proposed DeepPCT, a deep learning algorithm to identify PTM crosstalk using AlphaFold2-based structures. In this algorithm, one deep learning classifier was constructed for sequence-based prediction by combining the residue and residue pair embeddings with cross-attention techniques, while the other classifier was established for structure-based prediction by integrating the structural embedding and a graph neural network. Meanwhile, a machine learning classifier was developed using novel structural descriptors and a random forest model to complement the structural deep learning classifier. By integrating the three classifiers, DeepPCT outperformed existing algorithms in different evaluation scenarios and showed better generalizability on new data owing to its less distance dependency. AVAILABILITY AND IMPLEMENTATION: Datasets, codes, and models of DeepPCT are freely accessible at https://github.com/hzau-liulab/DeepPCT/.