Because of rapid economic development and urbanization, water shortage has become a serious problem in the arid region of China. To investigate urban water resource security, the supply demand pressure of water resources and the urban expansion index were analyzed under different developing scenarios in this paper. Based on the economic data of Urumqi, a typical inland city in the arid area, under the present development scenario from 2011 to 2030, a system dynamics model was constructed to simulate the water resource security. The results show that there will be great influence of urban expansion on water resource security in Urumqi in the future. Water resources are projected to become increasingly scarce if the urban expansion is left unchanged in terms of population, economic growth and water-use efficiency. To find a sustainable method for water resource use, four scenarios of urban expansion were set up based on the sensitive variables. Based on comparison of water consumption under the different scenarios, the harmonize scheme for urban water resource security is the best choice for the development of Urumqi. If the impact of urban expansion on urban water resource security alleviates in the future, the main parameters would have to reach a new standard of water use. Reducing the sewage and increasing the reuse proportion of wastewater are also very important for relieving the stress of water shortage. This research can serve as a reference for water resource allocation and urban planning in arid areas.