Cooperative and self-enforceable water allocation is a key instrument to manage geopolitical conflict induced by water scarcity, which necessitates concerning the cooperative willingness of the agents and considering their heterogeneity in geography, climate, hydrology, environment and social economy. Based on a multi-indicator system that contains asymmetric information on water volume contribution, current water consumption, water economic efficiency and efforts for eco-environmental protection, this study proposed a water allocation framework by combining the asymmetric power index approach with bankruptcy theory for solving the transboundary water allocation problem under scarcity. The proposed method was applied to the Yellow River Basin in northern China, which is mainly shared by nine provincial districts and frequently suffers from severe water shortage, and its results were compared with six alternative methods. The results highlight the necessity of quantifying agent’s willingness to cooperate under the background of asymmetric negotiation power when making decisions on transboundary water allocations. The proposed method allows to perform transboundary water allocations through simultaneous consideration of the agent’s cooperation willingness, asymmetric negotiation power as well as disagreement allocation points, which ensure the stability, fairness and self-enforceability of allocation results. Therefore, it can offer practical and valuable decision-making insights for transboundary water management under water scarcity.