Abstract The LHD experiment started in 1998 at the National Institute for Fusion Science and has continued for nearly 30 years. The experimental data obtained in these experiments are stored as physical data in the Kaiseki Data Server and made available to the public using an open data server. Through the experience of developing and operating this server, this paper discusses the problems that can occur in data management systems in long-term projects such as the LHD experiment and how they can be improved.