With the process of globalization and regional integration, the world today is increasingly interconnected and interdependent. Meanwhile, more transboundary issues are concerned with competition between countries for resources and environmental services, which involve the global economy, international trade, and national security of countries. Among these issue, geopolitical cooperation in international river basins highlights the development trend of transboundary eco-security. In this article we summarize the main transboundary issues and research advances, demonstrate cases of regulation and mechanism in transboundary eco-security of China. The results indicated that transboundary issues were brought into sharp focus by international rivers, and also were given close attentions on utilization of resources, protection of plants and animals, bioinvasion controlling and disasters monitoring. Interacting with global changes these multi- level issues intensify environmental risks in specific regions. For dealing with transboundary ecological issues, concepts of security as well as a higher-lever geopolitical cooperation need to develop. Furthermore, we put forward some recommendations for further study in the areas of transboundary water resources and climate changes, water security of inflow rivers, pollution in international river basins, interaction and impacts of large-scale engineering projects, combining the "Vision and Actions on Jointly Building Silk Road Economic Belt and 21st-Century Maritime Silk Road".