The way for spatial allocation of agricultural water resources is proposed with the concept of spot shadow price of irrigation system. Then certain problems on spatial allocation of water resources in China are discussed. Some results are given in this paper:The pricing system of agricultural water resources based on spot shadow price can raise utilization efficiency of water resources, attract input to irrigation system, and be helpful to form complete water market.Meanwhile, the pricing system, which is partly opposite to equity, needs to be adjusted in order to meet equitable objective.