Abstract: In recent years, International Fisheries Management Organization has played an increasingly important role in global fisheries governance. In order to further understand the current operation status of International Fisheries Organizations and promote their better international fishery governance, this paper takes five major International Fisheries Organizations (IFOs)—the Western and Central Pacific Fisheries Commission (WCPFC), Indian Ocean Tuna Commission (IOTC), International Commission for the Conservation of Atlantic Tunas (ICCAT), Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR), and International Whaling Commission (IWC)—as examples. Using fairness and efficiency as central criteria, the analysis focuses on member access, fundraising, internal governance, and cooperative communication. The results show that there are a series of problems in the operation process of International Fisheries Management Organization, such as fuzzy access standards, relatively single source of funds, unbalanced internal governance mechanism, low efficiency of consultation and decision-making, lack of supervision mechanism, and lack of depth of cooperative communication mechanism. In the future, access requirements should be strictly regulated and made more equitable to ensure fairness; expand the funding source of International Fisheries Organizations and improve the organizational independence; improve the internal governance structure of International Fisheries Organizations and set up a special external supervision body, establish a strong supervisory body to supervise the exercise of its power and the performance of its responsibilities, further improve the relevant international law, make comprehensive and systematic provisions on the powers and obligations of the International Fisheries Organization Committee in the form of law, establish a reward and punishment mechanism, and restrain the committee within the legal framework; strengthen the sense of cooperation among the member states, refine the cooperative measures and deepen the cooperative communication mechanism; further improve the operation efficiency of the organization and maintain the fair dimension of International Fisheries Management Organization. As one of the typical models of global fishery management, International Fisheries Management Organization plays a positive role in maintaining the international fishery order and promoting the sustainable development of fishery resources. This paper analyzes the current situation and problems of the operation mechanism of five International Fisheries Management Organization, which is of great significance for the systematic research of International Fisheries Management Organization and the construction of perfect operation mechanism.