High-throughput sequencing has the characteristics of complex experimental procedures, multiple quality control nodes, and a high proportion of bioinformatics technology. It is difficult to uniformly management and reuse the related detection samples and data. In May 2023, a tertiary hospital launched the construction of a localized high-throughput sequencing management system. Based on the design principles of security, friendliness, compatibility, and scalability, the management system had established three core modules: standardized data collection integration, clinical high-throughput sequencing full process management, and scientific research services, as well as a large clinical high-throughput sequencing database of hospital. By connecting with big data storage devices, local and third-party high-throughput sequencing detection platforms, sample libraries, and user terminals, this system broke down the data barriers of high-throughput sequencing related systems and devices, and met the different application scenarios of physician users, technician users, management users, and scientific research users in the hospital. As of October 2023, the system had been integrated with two high-throughput sequencing manufacturer devices in a public network environment and hospital information systems in an internal network environment, improving data retrieval efficiency and achieving closed-loop management of high-throughput sequencing detection projects preliminary, which can provided references for promoting the standardized management of high-throughput sequencing projects in hospitals in China.