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With the challenges of arid transboundary river water management among Central Asian countries, it is important to evaluate the water stress and propose practicable climate adaptation strategies. This study used the Syr Darya Basin (SDB) in a Central Asia data scarce region as the study area and, conducted the first quantified analysis of the spatiotemporal characteristics of water supply and requirements at the basin and irrigation district scale; identified its driving mechanisms based on systematic monitoring data concerning reservoir regulation and complex crop structure from 2000 to 2018; and a climate change scenario combined with a crop restructuring scenario was applied to evaluate water conservation effects and propose a climate adaptation strategy from 2019 to 2030. The results showed that runoff increased by 7.45 billion m3 but the water withdrawal decreased by 3.42 billion m3 after reservoir regulation in the basin during 2000–2018. Due to the unified water allocation, it was challenging to conduct and usually exceeded the plan by 0.4–8.5 %. The total crop water requirement (TCWR) mainly derived from cotton (61.5 %), winter wheat (12.1 %) and rice (13.9 %) increased by 3.15 billion m3 (+30.7 %) and the influence of crop area (380 million m3/a) was greater than that of climate (130 million m3/a). The wind speed (27.5 %) and rice area (19.2 %) also significantly contributed to the TCWR variation. The contradiction between water supply and requirement resulted in water scarcity in the basin. From 2019–2030, the water conservation effect of winter wheat (+20 %) under the restructuring scenarios reached 28.7 mm, which helped relieve water stress under the scenario of a 0.51–0.91 °C increase. Thus, priority planting of a winter wheat rotation and low water consuming crops is a practicable approach for coping with water scarcity and adapting to climate change in arid transboundary rivers of Centra Asia. [Display omitted] • A crop restructuring scenario was proposed to adapt to future climate change. • Increasing wind speed and rice area contributed the most to the water stress. • Priority development of winter wheat rotation is practical for water conservation. [ABSTRACT FROM AUTHOR]