Shaanxi Province is a region poor of water resources in China, and the lack of water resources is becoming a key factor which restricts the social and economic development of Shaanxi Province. In the perspective of efficient utilization of water resources, Shaanxi Province is committed to the transformation of the economic growth and the industrial structure, and treats these measures as important guarantees for the future development of Shaanxi Province. This paper focuses on building multi-objective programming model of industrial structure optimization under the limited water resources condition, indicates the direction of the industrial transformation and water consumption structural adjustment by solving the model, and furthermore points out the key factors that affect the development of Shaanxi Province in the future. Finally, the authors give some advices of promoting the reasonable and effective utilization of water resources of Shaanxi Province.