Vegetation carbon (VC) is a key indicator of the carbon cycle in terrestrial ecosystems, and the study of spatial and temporal changes in VC stocks at the watershed scale can better reveal the impacts of natural and human activities on VC stocks in watersheds, which will help in monitoring watershed ecological environments and to realize sustainable development in watersheds and regions. To reveal the spatial and temporal changes of the VC stock in the Urumqi River Basin, a typical arid zone basin, from 2001 to 2020, the spatial and temporal distribution characteristics of multi-year VC stocks in the Urumqi River Basin were estimated based on the Pixel Information Expert Engine platform, with MODIS (MOD16A17) as the main data source, and by combining methods such as trend analysis and the Hurst index, and analyzing the impacts of different factors on the VC stock by using a geo-probe to quantify the effects of the different factors on the VC stock. The results were as follows: (1) VC in the Urumqi River Basin has continuously increased in the last 20 years, the carbon stock in the whole basin has decreased sequentially from upstream to downstream, and there is expected to be a general trend of continuous improvement in VC in the basin in the future. (2) In terms of land use, the VC stock was largest in forest, followed by grassland, cropland, construction land, unutilized land, and finally water bodies. The VC of forest fluctuated and changed between 0 and 180 t C·km−2, while the carbon stocks of other land-use types fluctuated and changed between 0 and 90 t C·km−2. (3) Regarding the effects of topographic changes in the Urumqi River Basin on VC stocks, elevation and slope had the most obvious influence, with the VC stock rising with elevation showing an increasing trend, and the carbon stock fluctuating on different slopes. On flat land and with a slope direction of north, northeast, east, or southeast, the carbon stock increased; while with a slope direction of south, southwest, west, or northwest, the carbon stock decreased. (4) The interaction of temperature, land-surface temperature, land-use and land-cover change, and topography in the Urumqi River Basin has had a pronounced effect on VC over the last 20 years. The results are a valuable reference for further understanding and research on VC stocks and their mechanisms of influence in arid zones more broadly, as well as being of great significance for vegetation conservation and restoration efforts in the Urumqi River Basin specifically.