This study involved a comprehensive analysis of 256 PTC patients from Sun Yat-sen Memorial Hospital of Sun Yat-sen University (SYSMH) and 499 patients from The Cancer Genome Atlas. DNA-based next-generation sequencing (NGS) and single-cell RNA sequencing (scRNA-seq) were employed to capture genetic alterations and TME heterogeneity. A deep learning multimodal model was developed by incorporating matched histopathology slide images, genomic, transcriptomic, immune cells data to predict LNM and disease-free survival (DFS).