Green development is one important goal to achieve high-quality development in resource-based regions. A study of on the efficiency of green economy and its influencing factors under the spatial characteristics is of great practical significance to the interpretation of the spatial effect of green economy development in resource-based areas. Taking Xinjiang as an example, this paper uses the panel data of 14 prefectures and cities in Xinjiang from 2000 to 2017 to measure the green economic efficiency of Xinjiang. Based on the measurement results and the spatial correlation test, this paper further establishes a spatial econometric model to analyze the influencing factors and spatial spillover effects of the green economic efficiency in Xinjiang, and puts forward countermeasures and suggestions. The conclusions are as follows: there is a U-shaped relationship between economic development level and green economic efficiency in Xinjiang, the industrial structure and economic openness have significant negative impact on the improvement of local green economic efficiency, and a significant negative spatial spillover effect on the neighboring areas, urbanization level and labor productivity have significant positive effects on the improvement of local green economic efficiency and have significant positive spillover effects on the neighboring areas, independent innovation ability has insignificant positive effect on the improvement of local green economy efficiency and has significant positive spillover effects on the neighboring areas, education level has insignificant negative impact on the improvement of local green economy efficiency and has insignificant positive spillover effect on the neighboring areas. Therefore, it is of necessity to improve the economic policy system, optimize the industrial structure, and make the economy open wider to the outside world, the independent innovation ability more capable, and education level higher to improve the efficiency of green economy.