HQ IDS has been established as a part of MoD to carry out the role and functions vide Government of India, Ministry of Defence letter No Mod/IC/1027/32/IDS/5843/2001 dated 23 Nov 2001. The organisation is headed by the chief of integrated Defence Staff to the Chairman COSC (CISC) who enjoys a status equivalent to that of Vice Chief of a Service. The organisation has representation from all three services, MEA, DRDO and DoD and Def (Finance).

The envisaged role of the HQ has been organised into sets of coherent functions and matching organizational blocks in the form of Branches, Divisions (Divs) and Directorates (Dtes) have been established. The branches are headed by Deputy Chiefs of Integrated Defence staff (DCIDS) who are the rank of Lt Gen equivalence, the Division are headed by Assistant Chiefs of integrated Defence Staff (ACIDS) who are of Maj Gen Equivalence and Dtes are headed by Deputy Assistant Chief of Integrated Defence Staff (DACIDS).

Organisation of HQ IDS upto Branch heads is as follows-