The aim of studying the mode of inter-basin water transfer project water resource allocation is to search for an efficient allocation mechanism or rule, which makes water transfer project operation results achieve the maximization of social welfare. Based on the game theory and the institutional economics theory, this paper tried to describe the water resources allocation framework in the inter-basin water transfer project, and analysed different allocation mechanisms of water resource, then found an efficient allocation mechanism: firstly, our country clears and distributes the initial water rights, and then the water rights are allowed free trade on the market, which is a two-stage dynamic game model. This paper also provides an idea about incentive mechanism for inter-basin water allocation.