To address the data security issues faced by the National High Energy Physics Data Center, this paper analyzes the scientific data security risks faced by High Energy Physics Data Center based on traditional network security, and summarizes the characteristics of high energy physics science data security and proposes a data security management system, technical system, and operation system suitable for China's high energy physics science, aiming to provide reference and inspiration for the practical application of scientific data security issues. The system covers the entire data lifecycle, effectively ensuring the confidentiality, integrity, and availability of data during transmission, storage, and applications, preventing unauthorized access, theft, destruction, tampering, and leakage of security events.