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The increasing conflicts for water resources between upstream and downstream regions appeal to chronological insight across the world. While the negative consequence of downstream water scarcity has been widely analyzed, the quantification of influence of upstream water use on downstream water scarcity has received little attention. Here non-anthropologically intervened runoff (natural runoff) was first reconstructed in upstream, middle stream and downstream regions in China's 12 large basins in the 1970s to 2000s time period using the Fu-Budyko framework, and then compared to the observed data to obtain the developmental trajectories of water scarcity, including the ratio of water use to availability (WTA) and the per capita water availability (FI; Falkenmark Index) on a decadal scale. Furthermore, a contribution analysis was used to investigate the main drivers of water scarcity trajectories in those basins. The results show that China as a whole has experienced a rapid increase of WTA stress with surface water use rapidly increasing from 161 billion cubic meters (12% of natural runoff) in the 1970s to 256 billion cubic meters (18 %) in the 2000s, with approximately 65% increase occurring in northern China. In the 2000s, the increase of upstream WTA stress and the decrease of downstream WTA stress occurred simultaneously for semi-arid and arid basins, which was caused by the increasing upstream water use and the consequent decreasing surface water use in downstream regions. The influence of upstream surface water use on downstream water scarcity was less than 10% in both WTA and FI for humid and semi-humid basins during the study period, but with an average of 26% in WTA and 32% in FI for semi-arid and arid basins. The ratio increased from 10% in the 1970s to 37% in the 2000s for WTA and from 22% in the 1980s to 37% in the 2000s for FI. The contribution analysis shows that the WTA contribution greatly increases in the 2000s mainly in humid and semi-humid basins, while it decreases mainly in semi-arid and arid basins. The trajectories of China's water scarcity are closely related to socioeconomic development and water policy changes, which provide valuable lessons and experiences for global water resources management.