Ephemeral plants are a special plant synusia in the Gurbantünggüt Desert, which has attracted attention from ecologists due to its diverse species and significant role in ecology. To our knowledge, no research has analyzed the spatio-temporal patterns of ephemeral plants on a large-scale. Taking the Gurbantünggüt Desert -located in the central region of the Junggar Basin, northwest China-as the study area, and using remote sensing data, meteorological data, and field survey, this study explored the dynamic change in ephemeral plant cover in response to climate change on different spatio-temporal scales over the last 30 years. The results showed that, as far as the ephemeral plants synusia in the Gurbantünggüt Desert is concerned, the vegetation cover is low with simple community composition, high dominance, and low diversity, and the whole synusia undergoes an evident fluctuation in phenological change from early spring to summer. In addition to the phenological change in the ephemeral plant synusia, the normalized difference vegetation index (NDVI) in the desert also clearly fluctuates from early spring to summer, which is related to the life cycle of ephemeral plants. Using the phenological change characteristics of the ephemeral plant synusia, we extracted the NDVI during the phenological phases of ephemeral plants, and analyzed the spatio-temporal change of ephemeral plant cover from 1985 to 2014. In terms of spatial distribution, the highest cover area was in the south of the desert, followed by the mid-east and northern regions, with the western area showing the lowest cover area. With respect to temporal tendency, statistical analysis of the cover area showed that the ephemeral plant cover had a gradually increasing trend, which was attributable to an increase in temperature and precipitation during the research period. The highest cover area was in the oasis-desert ectone, which was due to the agricultural land located in this area. The artificial oases can supply sufficient surface water, which is beneficial for the growth of ephemeral plants. Conversely, the central desert region showed a low cover distribution pattern, which may be related to the lack of surface runoff and deep groundwater; the growth of ephemeral plants in the desert is completely reliant on atmospheric precipitation recharge. With respect to climate change, the spring temperature and precipitation showed an obvious increase from 1985 to 2014, and there was also an increase in winter precipitation. These notable increases in precipitation and temperature are of benefit to ephemeral plants. For yearly variation, the linear correlation coefficient indicated that NDVI was positively correlated with spring precipitation and winter precipitation. However, in terms of correlation coefficients, the NDVI was significantly positively correlated with winter precipitation (P < 0.05, r=0.405), whereas spring precipitation showed a weak positive correlation due to a time-lag effect. Moreover, according to an analysis of spatial differentiation of soil water content, climate change was not the key factor affecting the spatio-temporal change of ephemeral plants, but that the impact of human disturbance on the spatial distribution of ephemeral plants in local areas should be taken into consideration when assessing the large-scale spatio-temporal distribution of ephemeral plants. Therefore, in order to obtain a more accurate analysis of the dynamic change trends of ephemeral plants, future research will focus on human influence in local areas.