Most patients with papillary thyroid microcarcinoma (PTMC) have excellent prognoses with an indolent clinical courses. However, patients with lateral lymph node metastasis (LLNM) may experience higher locoregional recurrence rates and poorer prognoses. Therefore, it is crucial to establish an effective preoperative stratification strategy to reliably assess the risk of LLNM. PTMC samples were obtained from Peking Union Medical College Hospital. The data-independent acquisition mass spectrometry proteomics technique was used to identify protein profiles on PTMC tissues with and without LLNM.