With the rapid economic development of the Xinjiang Uygur Autonomous Region, the area’s transport sector has witnessed significant growth, which in turn has led to a large increase in carbon dioxide emissions. As such, calculating of the carbon footprint of Xinjiang’s transportation sector and probing the driving factors of carbon dioxide emissions are of great significance to the region’s energy conservation and environmental protection. This paper provides an account of the growth in the carbon emissions of Xinjiang’s transportation sector during the period from 1989 to 2012. We also analyze the transportation sector’s trends and historical evolution. Combined with the STIRPAT (Stochastic Impacts by Regression on Population, Affluence and Technology) model and ridge regression, this study further quantitatively analyzes the factors that influence the carbon emissions of Xinjiang’s transportation sector. The results indicate the following: (1) the total carbon emissions and per capita carbon emissions of Xinjiang’s transportation sector both continued to rise rapidly during this period; their average annual growth rates were 10.8% and 9.1%, respectively; (2) the carbon emissions of the transportation sector come mainly from the consumption of diesel and gasoline, which accounted for an average of 36.2% and 2.6% of carbon emissions, respectively; in addition, the overall carbon emission intensity of the transportation sector showed an “S”-pattern trend within the study period; (3) population density plays a dominant role in increasing carbon dioxide emissions. Population is then followed by per capita GDP and, finally, energy intensity. Cargo turnover has a more significant potential impact on and role in emission reduction than do private vehicles. This is because road freight is the primary form of transportation used across Xinjiang, and this form of transportation has low energy efficiency. These findings have important implications for future efforts to reduce the growth of transportation-based carbon dioxide emissions in Xinjiang and for any effort to construct low-carbon and sustainable environments.