As a national joint-use facility, the D3 Center provide large-scale computing systems, such as supercomputers, to researchers at universities and research institutes across Japan, enabling computation and information processing for academic research and education.

The Joint Usage/Research Center for Interdisciplinary Large-scale Information Infrastructures (JHPCN) is a network-type joint usage and collaborative research infrastructure (approved by the Minister of Education, Culture, Sports, Science and Technology) consisting of eight universities that own supercomputers, with the University of Tokyo's Information Technology Center serving as the core institution. The D3 Center acts as one of the constituent centers and accepts joint research proposals from researchers nationwide.

The High-Performance Computing Infrastructure (HPCI) is an innovative shared computational environment that connects major supercomputers and storage systems at universities and research institutes across Japan via a high-speed network, catering to diverse user needs. The D3 Center is a resource provider within HPCI, offering computing resources such as supercomputers and storages systems.

The mdx platform is a cloud-based (virtualized) data infrastructure focused on data utilization, jointly operated by nine universities and two research institutes, including the University of Tokyo's Information Technology Center. The D3 Center participates in mdx and provides the cloud computing infrastructure known as mdx II.