Objective: To analyze the clinical characteristics of SCCUP and to assess the changes in diagnosis and treatment under standardized diagnosis mode as well as factors affecting patient prognosis. Methods: The clinical data and follow-up data of 51 SCCUP patients admitted in our hospital from September 2003 to September 2023 was collected. Factors related to the overall survival (OS) and regional control (RC) were also analyzed. Results: Of the 51 patients, the majority were male, with an average age of 59.96±10.29 years. At the end of follow-up, there were 22 deaths and 17 recurrences and 27 primary lesions appearance. For EBER-P16-SCCUP, primary lesions detected afterwards and extracapsular invasion are 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. Actively searching for the primary lesion positively impacts patient prognosis.