The NCHC is one of the 12 national-level member laboratories, and a major operating component of the National Applied Research Laboratories (NARL). The Director of the NCHC serves as its head. He is assisted by two Deputy Directors. 

In order to best support its HPC and networking services, the NCHC is divided into 10 divisions: Administration , Training and Promotion , Planning and Service , Computing Technology Integration, Computational Engineering , Scientific Computing, Data Computing, Software Technology, Network and IT Security and Computing Facility.