Vegetation coverage is an important indicator of the terrestrial ecosystems, and it provides crucial significance for evaluation and analysis of vegetation change. The Shule River Basin is a typical ecological fragile region in the inland of Northwest China. We used vegetation coverage index as given in Technical Specifications for Assessment of Ecological Environment. Geographic information system (GIS) spatial analysis was used to analyze the temporal and spatial features of vegetation cover in the Shule River Basin and its influencing factors from 1986 to 2011. The results showed that vegetable cover is very low in most areas of Shule River Basin with only the upstream parts of the oasis and watershed haven high vegetation cover. The average vegetation coverage index increased from 6.78 to 8.31 during 1986–2011. An area of 59,998 km² in the Shule River Basin has unchanged vegetation coverage index and this account for 51.7% of watershed areas for the period of the study. Also, an area of 31,721 km² recorded an increased vegetable cover, accounting for 27.3% while an area of 24,372 km² decreased vegetation cover which accounts for 21.0%. There was different correlation between vegetation cover and annual precipitation in the Shule River Basin.