The realization of regional sustainable development has been a popular research topic during the process of urbanization. To explore the coordination relationships between urban development and ecological security-taking Urumqi city, a representative arid city in Xinjiang, China, as a study area-this study has constructed a framework of spatial suitability evaluation based on the characteristics of a Mountain-Oasis-Desert System (MODS) in an arid area under the framework of major function oriented zoning (MFOZ). A spatial overlay analysis using Geographic Information System (GIS) with a 5 m × 5 m grid or towns and streets as the basic unit was applied to comprehensively evaluate spatial suitability. The results showed that the study area was zoned into a forbidden development zone (as patches set in towns and streets), an ecological protection zone (nine towns or streets), a moderate development zone (16 towns or streets), and a key development zone (82 towns or streets), accounting for 30.35%, 32.50%, 23.79%, and 13.36%, respectively. The zoning results provided a basis to pointedly put forward the development and protection strategies of each administrative unit; and the research framework can be applied to other arid areas for the decision-making related to the urban space layout and environmental management.