We recruited 646 participants, including healthy individuals, patients with benign nasopharyngeal diseases, and NPC patients for plasma cell‐free DNA(cfDNA), which underwent low‐depth whole‐genome sequencing (WGS) to extract multi‐dimensional molecular features, including fragmentation pattern, end motif, copy number variation(CNV), and transcription factors(TF). This evidence concerns the gene TF and nasopharyngeal carcinoma.