In order to explore how to break through the collective action of water resources cooperation management in the Rhine River Basin countries, this paper analyzes the governance dilemma in the process of cooperation and key elements. The issue of water pollution in the Rhine River Basin has risen from a common environmental issue to an international political issue and then become a political commitment of the countries along the river. It has experienced a long process of stakeholders competing and gaming with each other. The trade-offs between economic development and environmental protection, and high costs caused by externalities and uncertainty become difficulties for cooperation. The key factors to break through the cooperation dilemma are the degree of problem pressure, the participation of non-governmental actors, the flexibility of system, the homogeneity of social politics and economy, and the stock of social capital. In the utilization, development and management of water resources in cross-border basins, China should pay attention to establish a dialogue and communication mechanism, provide a cooperation platform and cultivate mutual trust, advocate multi-center institutional arrangements, maintain institutional flexibility, strengthen the construction of water quality monitoring and early warning networks, guide public participation and play the role of public supervision.