CNFI is operated by a board composed of sixty Directors and twenty Supervisors. Fifteen Standing Directors and five Standing Supervisors are further elected among the Directors and the Supervisors, and the Convener of Board of Supervisor then elect one Chairperson and three Vice Chairpersons. With the approval of the Board of Directors, the Chairperson appoints the Secretary General and Deputy Secretary Generals. In addition to the Office of the Secretary, there are Comprehensive Planning Division, Business Division, Member Affairs Division, General Affairs Division, Foreign Affairs Division, Intellectual Property Division, Mainland China Affairs Division, and Finance Division.

Various committees are established to help Taiwanese enterprises deal with rapidly changing business environment. The leading industrialists, entrepreneurs, scholars, and experts are invited by the Board to serve on these committees for the purpose of researching on critical issues that affect both the private and public sectors.