In the era of big data, the storage of massive amounts of data has become a challenging problem. DNA storage technology, as a cutting-edge solution to this challenge, particularly focuses on the development and challenges of information editing technology. Initially, DNA storage primarily served “cold” data, but the latest advancements in the technology have driven its development towards supporting data updates and management for more advanced applications. This paper proposes an incremental management method for secure DNA storage, designing a hybrid encryption mechanism that supports multi-party editing and a DNA incremental storage model. While ensuring security, this model achieves secure and efficient information editing and management under existing technological constraints through a partitioned storage scheme and efficient indexing encoding. This approach meets the modern data management requirements for flexibility and cost-effectiveness, providing new perspectives and strategies for addressing core issues in DNA data management.