As a major resource region, Xinjiang is both China’s energy security base and an important hub connecting Asia and Europe. Following the country’s call for carbon emission reduction, the Xinjiang government proposes to accelerate the construction of eight major industrial clusters in 2023. The concept of sustainable development is also reflected in the industrial clusters in areas such as new energy. In this study, we combined panel data from 14 regions and cities in Xinjiang from 2006 to 2020 and analyzed the synergy between the development of industrial clusters, carbon emissions, and economic growth using a coupling coordination degree model. Subsequently, we used the super-efficiency slack-based measure (SE-SBM) and Dagum’s Gini coefficient to analyze the spatial disequilibrium of efficiency measures and efficiency cases. The results show the following: (1) Overall, the industrial clusters, carbon emissions, and economic growth in the 14 regions and cities of Xinjiang are not well coordinated. The best reported level has been medium coordination, but there exists a certain degree of correlation among the three. (2) Low-carbon economic efficiency under the influence of industrial clusters in the 14 regions and cities shows significant regional differences. The regions and cities with low-carbon economic efficiency greater than 0.8, which is significantly better than the other regions in terms of efficiency, are all located in northern Xinjiang. (3) During the study period, the overall regional difference in low-carbon economic efficiency under industrial clusters in Xinjiang decreased from 0.183 to 0.17. However, the regional differences were still large. The conclusions indicate that policies for industrial clusters in Xinjiang can promote industrial development, and there may be a correlation between them and the low-carbon economy. This will effectively contribute to local sustainable development. However, overall regional differences are significant, and the degree of coordination is low. Therefore, we suggest that the government can share the advantages of development by constructing cross-regional cooperation platforms. At the same time, the Xinjiang government should make full use of the rich local wind and solar energy resources and explore a low-carbon path toward transforming the traditional energy industry. It can also be seen that industrial clusters in Xinjiang can effectively promote local sustainable development.