The ecological capital is unique but the ecological carrying capacity is limited in Arid Region. The supply-demand relationship and the equilibrium mechanism of the ecological footprint have received much attention. The Manas River Basin, a typical inland river basin in the arid area, was taken as the target area. According to the characteristics and change trend of land use/cover type in the arid area, we established a three-dimensional ecological footprint evaluation model based on the ecosystem service flow law generated by the oasis production consumption. We analyzed the spatial and temporal differences of the ecological footprint of the river basin from 2000 to 2018 by using the local parameters of the arid area. The results showed that: (1) due to the interaction of limited natural carrying capacity and social and economic development, the ecological deficit of the Manas River Basin is expanding. On the time scale, the basin ecological deficit has increased by 4.36 times in the past 18 years, and the per capita ecological deficit has increased by 3.12 times, among which the proportion of energy land and cultivated land was high and the growth rate was fast, and its contribution to the ecological deficit was far more than other types. On the spatial scale, the contribution rate of Shihezi city to the basin ecological footprint was significantly higher than that of Shawan County and Manas County. (2) In the same period, the ecological footprint span of the Manas River Basin increased by 0.59 times, the depth of the footprint increased by 0.44, and the ratio of span to depth reached 3343876:1.63, indicating that the occupation of the flow capital was increasing, the stock capital is declining, and the ecological pressure was increasing. (3) The utilization efficiency of basin resources has been significantly improved, increased by 4.73 times in 18 years, and the growth rate was 5778.3 yuan/hm²/year. (4) Although the basin faced great ecological challenges and population pressure, it was not prominent in the whole Xinjiang. Compared with the provincial and national parameters, the local parameters can better reflect the current status of natural capital use in the river basin. Finally, the optimization prospects of ecological capacity in the arid area and suggestions for sustainable development of the river basin are proposed.