How to depict the circulation mechanism of natural resource consumption among regions and its impact on ecology is a difficult point to measure the sustainable development of regions. This paper adopts the improved three-dimensional ecological footprint model and introduces the utilization ratio of stock-flow and the occupancy rate of capital flow. Then the model is used to calculate the three-dimensional ecological footprint of the Xinjiang region from 2003 to 2018, and measure the degree of natural capital utilization in various states and cities in Xinjiang. Focusing on the differences in the use of natural capital in the south and the north of Xinjiang, partial least squares (PLS) is applied to find out the causes that affect the changes of ecological footprint. At last, Gini coefficient and difference coefficient are employed to quantify the degree of economic difference between the south and the north of Xinjiang, and the sustainable development trend and the difference between the south and the north of Xinjiang are explored from the natural and economic perspectives. The results show that: ① Xinjiang's per capita ecological footprint continued to grow from 2003 to 2018, with a growth rate of 119.94%. The ecological carrying capacity per capita is basically maintained at about 1.7 hm². The occupation intensity of flow capital increased continuously, and the ecological deficit problem became more and more serious. ② During the research period, there were obvious spatial differences in the growth range and speed of ecological footprint in the southern and northern Xinjiang, showing a trend of "high in the north and low in the south". The ecological deficits of various states and cities show different degrees of growth. The high-value areas are Karamay City in northern Xinjiang and the economic belt on the northern slope of Tianshan Mountain. ③ The added value of the primary industry has the most significantly positive driving effect on the ecological footprint, while the added value of the tertiary industry has the reverse driving effect on the ecological footprint. ④ From 2003 to 2018, the Gini coefficient in the southern and northern parts of the Xinjiang remained between 0.4 and 0.5, which was at the level of medium warning degree. The regional economic difference coefficient in the southern and northern parts of the Xinjiang did not change much, and the regional economic difference coefficient in the northern part of the Xinjiang was significantly higher than that in the southern part of the Xinjiang.