Objective To identify the biomarkers of papillary thyroid carcinoma and explore the possible pathogenic mechanism. Methods The cancer tissues of 5 patients with papillary thyroid carcinoma and adjacent normal thyroid tissues were analyzed for protein expression by TMT proteomics technology. Differentially expressed proteins were screened and identified, and functional annotation of differentially expressed proteins was carried out by bioinformatics and pathway enrichment analysis. Results A total of 639 differential proteins were identified, including 278 up-regulated proteins and 361 down-regulated proteins. Among them, six up-regulated proteins are expected to become specific markers of PTC. Conclusion Based on the above research results, differential proteins may become new molecular markers of papillary thyroid carcinoma, and these differential proteins and their enrichment pathways can provide new insights into its pathogenic mechanism ideas and directions.