The scientific data center is the carrier of scientific data, the foundation and guarantee environment for the security of scientific data resources, and undertakes the mission of promoting the open sharing of scientific data. The security of scientific data mainly depends on the security management of the scientific data center. This paper focuses on the data security work practice of the National Cryosphere Desert Data Center(referred to as NCDC), analyzes the sources of security issues in NCDC, proposes a data center security capacity building model that includes three dimensions: work hierarchy, security process, and security object. proposes a security management approach that focuses on prevention and full process control, and analyzes the main prevention contents of physical security, network security, system security, application security, and data security in NCDC, and corresponding security management measures were designed for these main security objects, security capacity building was carried out, and data security management work was achieved on the basis of overall development of NCDC. The experience of data center security practice in the past 10 years was summarized, and these experiences have certain reference significance for the security management of other scientific data centers.