Objective To investigate the clinical characteristics of metastatic squamous cell carcinoma of cervical lymph nodes with unknown primary site (SCCUP), evaluate the effect of standardized diagnosis and treatment mode on the diagnosis and treatment of SCCUP, and analyze factors affecting the prognosis of patients. Methods A total of 51 SCUPP patients admitted in our hospital from September 2003 to September 2023 were included. Their clinicopathologic data, preoperative examination, treatment plan, follow-up of primary site, 5 years overall survival rate (OS) and regional control rate (RC) were analyzed comprehensively. Results Of the 51 patients, 47 were males and 4 were females, with an average age of (59.96±10.29) years. By the end of follow-up, there were 22 cases of death, 17 of relapse, and 27 of primary lesions during follow-up treatment. For EBER(-) p16(-) SCCUP, primary lesions detected afterwards and extracapsular invasion were independent risk factors affecting OS. Conclusion The introduction of EBER and p16 for SCCUP allows for a more rational classification and more appropriate diagnostic and treatment approaches for patients, and the active investigation of primary lesions has a positive effect on the prognosis of patients.