With the continuous expansion of drylands in the context of global climate change, governments have implemented a series of greening policies such as afforestation, to reduce ecological degradation. However, owing to historical conditions and technical constraints, few attempts have been made to quantitatively assess the differences in carbon sequestration capacity and the associated environmental controls among major ecosystems in the arid and semi-arid areas. Based on six flux towers located in northwestern China measuring the carbon fluxes in a maize (Zea mays L.) cropland, alpine meadow, wetland, swamp meadow, Tamarix, and gobi desert, this work revealed that all ecosystems sequestered CO₂ at various magnitudes. The cropland had the highest carbon uptake, followed by the alpine meadow, swamp meadow, wetland and Tamarix, respectively. Distinct seasonal dynamics in carbon sequestration were observed across these ecosystems with the peak values in summertime, whereas the gobi desert exhibited as a weak carbon sink with considerable fluctuations around the year. In this water-limited region, soil water content instead of rainfall, is expected to be the primary environmental control on the land–atmosphere carbon fluxes, and regarded as a key linkage between hydrologic and ecologic processes. Therefore, not only the appropriate vegetation types, but also the water availability controlled by the local climatic constraints and soil characteristics, should be addressed in order to identify management strategies for ecological restoration in the dry areas.