The IHS is organized as an association (Verein), following Austrian jurisdiction. Its main decision-making body is the Board of Trustees (Kuratorium), consisting of nine members. Advising roles are taken by the Scientific Advisory Board and the Stakeholder Committee.

The Institute has a two-level structure. It is managed by the Director (Prof. Dr. Martin Kocher) and a General Secretary (Ralf Böckle, MPA). Its research tasks are carried out by Research Groups and Competence Centers. Many projects are conducted by teams across research units.

The research units receive support from administrative and service units, such as the IT, Library, Head Office and Finances.