Accurately portraying the mechanism of the flow of natural resource consumption between regions and its impact on ecology is of crucial value in deepening the understanding of the coordinated relationship between population, resources, environment and development. Consequently, this promotes the sustainable development of the natural economy and society. Based on a regional-industrial perspective, this study used a localized three-dimensional ecological footprint model to measure and decompose natural resources in Xinjiang from 2005 to 2020. In doing so, the study clarified the supply, demand, and flow utilization of natural capital in Xinjiang, the balance of spatial and temporal allocation of resources, the coupling between economic growth and resource consumption, and the coordination between industrial structure and ecological environment. The results showed that (1) Xinjiang's per capita ecological deficit grew from 2.096 to 11.667 in 2005–2020. Moreover, the energy footprint was a decisive part of the ecological deficit throughout the study period. Furthermore, the trend of increased ecological pressure was higher in northern and eastern Xinjiang than in southern Xinjiang. (2) The overall Gini coefficient of Xinjiang's ecological carrying capacity was at the critical value of spatial equilibrium (0.4), with differences between the groups: Northern & Southern Xinjiang > Northern & Eastern Xinjiang > Eastern & Southern Xinjiang. The reasons for this inter-regional economic disparity are related to fiscal expenditure/GDP, level of urbanization, and regional industrial output. Overall, the decoupling relationship between environmental pressures and economic growth was optimistic. (3) From an industrial perspective, the levels of industrial structural efficiency and the industrial ecological harmony index were still relatively low, but the overall trend was on the rise. (4) Resource endowment, economic development, consumption structure, and population had significant driving effects on the ecological footprint, whereas environmental protection, science, and technology could inhibit its growth to a certain extent. This study aimed to provide an in-depth analysis of the current situation and problems of natural resource use in Xinjiang and provide theoretical and practical references for sustainable development in the region.