As a major component of land ecological systems, vegetation is generally considered a sensitive indicator of climate change. This study makes use of GIMMS-NDVI3g, as well as conventional climate data observed on the ground by the China Meteorological Administration, to study the spatio-temporal variations and driving factors of vegetation cover during the period from 1982 to 2013 in the "mountain-oasis-desert" coupled system of Xinjiang and its 11 sub-systems including mountains, oasis, plains, and desert. The coefficient of variation is used to study the variability of vegetation cover in this representative system; the Theil-Sen median analysis and Mann-Kendall trend test are used to investigate the vegetation cover patterns and trend in this system; the results obtained from the Hurst index are integrated to study the sustainability of the NDVI pattern in this system. This study demonstrates that 1) the temporal-spatial vegetation cover for the mountain-oasis-desert system shows great differences in different ecoregions and the mountain and oasis regions generally show an increasing trend in each year. 2) In 32 years, the vegetation cover in Xinjiang shows variation at a medium level (average value of CVNDVI is 0.116) and a higher spatial variation in the desert than the oasis and mountain regions; 3) the vegetation cover in each ecoregion of the mountain-oasis-desert system exhibits a trend of improvement or degradation and the vegetation cover trend in the oasis and mountain subsystems have clearly improved. 4) The vegetation cover sustainability of the mountain-oasis-desert system also shows great differences among the different ecoregions; the desert vegetation cover in this system exhibits sustainability and a degradation trend but the vegetation cover of the oasis exhibits a trend of sustainable improvement. In addition, the variations trend of the vegetation cover in the mountain areas shows obvious regional differences. 5) The comprehensive analysis of the vegetation cover variations in different ecoregions of the typical system demonstrates that the vegetation cover variations are affected by the combined or synergetic action of hydrothermal conditions such as temperature, precipitation, as well as humidity. In addition, the fluctuations in the vegetation cover in this system are the result of the combined action of temperature and precipitation (r = 0.35, p < 0.05). The vegetation cover trend of this system is significantly affected by precipitation (r = 0.22, p < 0.05). The climate in this system has changed to warmer and wetter conditions, which has improved the vegetation cover in this typical system (r(al) = -0.20, P-al < 0.05; r(temp) = 0.21, P-temp < 0.05). In addition, the sustainability of the vegetation cover in this system results from the combined effect of temperature and precipitation (r = 0.38, p < 0.05). This study on the variations in the NDVI spatial patterns for the mountain-oasis-desert system is of great theoretical and practical significance for studies of arid areas.