The cooperative governance of international rivers has become an important way to promote China’s neighborhood diplomacy. Many scholars have stressed that China should attach importance to inter-regional water resources cooperation mechanisms. However, China lacks the corresponding experience in designing such international river basin organizations. Therefore, China needs to understand the successful experiences and lessons of failure of international river basin organizations while continuously reviewing its own practical experiences. Based on these requirements, this study took the international river basin organization data collected by the Transboundary Freshwater Dispute Database (TFDD) as the research object, and expounded their development history, current situation, and other basic issues. The results show that the history of the international river basin organizations can be divided into three stages. International river basin organizations differ in organizational function, organizational category, structural characteristics, and governance mechanism. This study also reviewed the situation of the international river basin organizations in China and identified three key points with reference to international experiences. The design and selection of international river basin organization in China should fully respect the regional differences of the northeast, the northwest, and the southwest regions. At the same time, it is necessary to improve the daily management and emergency management capabilities of river basin organizations in China from the perspective of organizational structure and governance mechanism. However, the establishment and improvement of international river basin organizations is a long-term endeavor. It needs to adapt to the development stage of China’s cooperative development of international river basins. In particular, it needs to learn from the failure of many developing countries and establish a new type of international river basin organization under the vision of one community.