Omics big data is a significant foundational and strategic resource for the country, which plays an important role in supporting the basic research and application innovation of life sciences, promoting the innovative development of bioeconomy, and maintaining national security. With the rapid accumulation of omics data, the security of data management has become increasingly prominent. Facing the major strategic needs of China's population health and sustainable social development, the National Genomics Data Center (NGDC) has established a comprehensive research architecture for collecting, storing, managing, sharing, and mining of big data in omics, forming a series of practices and measures for the security management of the data. This paper delves into the issues of security management of omics big data throughout its lifecycle, elaborating on NGDC's security management measures implemented in the collecting, storing, managing and sharing of the data. Furthermore, it summarizes NGDC’s achievements in the security management of omics big data. Finally, this paper envisions the future directions for the security management of omics big data, including enhancing the data classification and categorization system, enhancing data hierarchical security management technologies and strengthening the construction of off-site disaster recovery, in order to achieve the security management and sustainable development of omics big data in life sciences.