Based on the background of water distribution of Heihe River, it analyzes the urgent situation of water shortage and the effects of the land use structure on it in the middle reaches of Heihe river after water distribution. Because of the close correlation of the rational application of water and land resources in the arid area, reasonable land use structure can make water more effectively used. Due to the above reasons, it argues that the water shortage restriction should be solved by reasonable optimization of land use structure; in addition, it also puts forward the main direction of land use optimization.