The energy-rich area of the Yellow River basin are the major energy producers in China, the energy eco-efficiency (ecological efficiency) of this area has a direct impact on the implementation of ecological protection and high-quality development strategies in the Yellow River Basin due to its huge energy consumption. In this paper, the Stochastic Frontier Model (SFA) was used to estimate the energy ecological efficiency of the study area from 2002 to 2016, the spatial differences in energy eco-efficiency were explored with the use of Spatial Auto-regressive Model (SAR), the Spatial Dubin Model (SDM) is used to analyze the influencing factors. The results show that the average value of each region in 2002 and 2016 is 0.799 and 0.698 respectively; the energy eco-efficiency showing significant spatial aggregation, with the lowest in western regions such as Wuzhong and Zhongwei, and the highest in central regions such as Ordos and Yulin; the spatial pattern of energy eco-efficiency is affected by many factors, such as the proportion of fixed assets investment in gross regional product, industrial added value in gross regional product, and the foreign investment. As a result, the formulation of regional development strategies shall focus on optimization of industrial structure and improvement of regional technical level, which shall also be supported by the establishment of cross-regional coordination organizations, the best play of advantages of all regions, and the improvement of industrial competitiveness, so as to realize the evolution and improvement of the overall energy eco-efficiency in the region.