It is important to understand the carbon-water cycle, which accurately reflects the temporal and spatial variabilities in ecosystem water use efficiency (WUE). In this study, the Mann-Kendall (MK) test was used to study the variabilities in the spatial patterns of the gross primary production (GPP), evapotranspiration and WUE across Central Asia [the Xinjiang Uyghur Autonomous Region (XJ) in China (CHN), Kazakhstan (KAZ), Turkmenistan (TKM), Uzbekistan (UZB), Kyrgyzstan (KGZ), and Tajikistan (TJK)] from 2000 to 2014. We compared the change results by country, land cover type, population density, and human influence. In addition, the results of GPP, evapotranspiration (ET), and WUE parameter tests were combined and classified to analyse the causes of the changes in WUE. The results showed that (1) the time series of GPP, ET and WUE exhibited no significant changes. The spatial distribution of the WUE exhibited significant increases in the northern part of KAZ, the Ili Valley and the alpine region in KGZ and exhibited decreases in south Xinjiang and the irrigated area of UZB. (2) The main land cover types that exhibited changes in WUE were farmlands and grasslands, and areas with a medium population density exhibited large WUE changes. (3) The increased WUE resulted from an increased GPP and decreased ET. The increased GPP was because of increased precipitation and the Green for Grain Project, and the decreased ET was due to the response of vegetation to drought stress; the decreased WUE was mainly caused by changes in the crops planted and unreasonable water use practices in the irrigated agricultural areas in Central Asia. This study, which is based on the variabilities in WUE spatial patterns, should provide a theoretical basis for ecosystems in arid land areas.