Tibet in China has extremely a fragile natural ecosystem, which is under a great pressure from global changes. The carbon footprint (CF) and water footprint (WF), reflecting the pressures of regional development on the natural environment, represent a lacuna in the field of study in Tibet due to missing data. In this paper, the 2012 multi-regional input–output table of China was employed to quantify the CF and WF of Tibet and the relationship between Tibet and other provinces of China. Spatial pattern and key sectors were also studied to demonstrate the current characters and the future trend of footprints. Tibet’s carbon emission was 4.0 Mt, 32.7% of CF, indicating that Tibet was a net importing region of carbon emission. Tibet received embodied carbon emission by trade from other regions, especially from Hebei, Inner Mongolia and Henan provinces, but played a complex role in virtual water allocation by transferring to most provinces and receiving from some provinces. The CF of Tibet will increase under different scenarios of 2030, but the WF can be restricted to 2.5 Gt in the slow scenario. In the future, imports of virtual resources will benefit the fragile ecosystem of Tibet and moreover, it is vital to restrict the local resource-intensive sectors and improve resource-use efficiency.
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