This paper applies the inventory model of the monopoly firm to establish a regional water transfer management institution behavior analysis model. The behavior analysis model uses stochastic dynamic mechanism to find out the optimal water transfer price under the condition of uncertainty demand and supply of water resources. This model assumes the regional water transfer management institution could reserve water resources for cross-term usage and borrow water from other regional water management institutions when its reserved water is insufficient. The results of this paper show that 1) the water administration authorities should not set up a rigid water transfer price management mechanism. 2) The regional water transfer management institution is supposed to dig ditches and ponds to reserve water, or to rent rice fields for fallow in order to reserve water. And 3) correct weather and rainfall predictions as well as the demand function of water resources in all industries; will make the distribution of water resources more effective.