To further reduce flood damages and to solve regional drainage disputes, on the basis of exploring the connotation of the flood drainage right, it is concluded that the flood drainage right is mandatory, exclusive, tradable, variable and urgent. The WSR analysis framework for the allocation of flood drainage rights is established by using the WSR system method. It is regarded that the allocation of flood drainage rights is subjected to physical, reasonable and artificial factors. The functions of the above factors are analyzed during the allocation process, and an index system for the initial allocation of regional flood drainage rights is established. This will help to systematize and stratify the driving factors for the effective initial allocation of flood drainage rights so as to provide the reliable basis and the decision-making of flood control and to play a supporting role in guaranteeing the safety of flood control and realizing the social fairness and regional sustainable development.