Water resources are the most critical influencing and limiting factor for ecosystem and socioeconomic development in arid zones. To mitigate ecological degradation in the lower reaches of inland rivers across arid regions, managed water redistribution has been widely implemented as a key anthropogenic intervention in drylands globally. The trade-off between water consumption and carbon sink benefits resulting from anthropogenic water resource allocation has then become an urgent scientific issue. The results showed that the trend of NPP increased from -1.5455 to 1.8611 gC/m2/a after the ecological water transfer. Among different vegetation types, forest land exhibited the highest carbon sequestration capacity, followed by farmland and grassland. Following the ecological water transfer, the total carbon stock in the input area increased from 21.97 in 2010 to 23.38 Tg in 2020. The implementation of ecological water diversion policies has markedly enhanced the carbon sink function in the lower reaches of the Shiyang River. However, the water cost per unit of carbon sequestration achieved was found to be substantially higher than the global average. Therefore, from the perspective of basin water-carbon balance, there is some room for discussion and optimization of the ecological water transfer policy in the arid zone.