Abstract: Provincial initial water rights and basinlevel government reserved water rights are indispensable parts of basinlevel initial water rights. Research on the coupling coordination between the two subsystems is an effective way to improve the efficiency of water resources usage. According to the requirements of Strictest Water Resources Management System (in China), the criterion of “Three Red Lines” for coupled water allocation was established to judge the harmonity of the coupling coordination of the two subsystems for the perspectives of water amount, water quality and water use efficiency. If the basin-level water allocation failed to satisfy the coupling harmonity of the two subsystems, the individual allocation solution of the two subsystems is adjusted until the coupling harmonious solution is reached and the solution of basinlevel initial water rights allocation is obtained. The overall feasibility and effectiveness of the proposed model was demonstrated by the application to the case study of Taihu Basin in China. This study may provide important reference for similar research in other river basins