Purpose <p>This study proposes a framework to address challenges in securing scientific data storage, tailored to China's changing technology and regulations, and offers strategic security advice for managing scientific data systematically.</p> Methods <p>The framework is constructed based on analyzing existing management measures and technological strategies for scientific data storage security, with a specific emphasis on distinct storage phases. A four-phase storage model (temporary, application service, long-term, and general storage) is proposed mapping to scientific data workflows, incorporating five core security dimensions: regulatory compliance, system robustness, network integrity, media protection, and personnel governance. The framework has been iteratively refined and deployed at the National Basic Science Data Center and is designed to adapt to diverse storage environments while prioritizing scalability and compliance with data governance standards.</p> Conclusion <p>The framework provides systematic, scalable strategies to enhance data protection, mitigate risks, and support compliance in China’s dynamic scientific data ecosystem. Its modular design allows tailored deployment facilitates data application services via the National Basic Science Data Platform and securing exascale datasets security at Large-Scale Research Infrastructures.</p>