As global problems such as the lack of resources and environmental degradation continue to intensify, the international community is increasingly aware of the importance of green development. At the same time, as a crucial guideline for China’s ecological civilization construction, “Beautiful China” development, and global economic transition and restructure, green development will surely become the important engine for the green transformation and development of the Jing-Jin-Ji region and the whole country. Based on a thorough review of the concept of green development, this paper estimates the green development efficiency of 13 cities in Jing-Jin-Ji region of China in 2003-2017 by using the super efficiency SBM model. Then, by employing the coefficient of variation and the Global Moran’s I, this paper further explores the spatio-temporal differentiation characteristics of the green development efficiency. Finally, the spatial panel model is used to explore the influencing factors of the green development efficiency. The results show the following: (1) The overall green development efficiency in Jing-Jin-Ji region of China declined steadily by 2% from 0.965 in 2003 to 0.948 in 2017. (2) The green development efficiency basically presents the spatial differentiation characteristics of the higher in the northern cities and the lower in the southern cities. (3) The green development efficiency has significant regional differences, and increased by 22% from 0.240 in 2003 to 0.295 in 2017. (4) Economic development level influence on the green development efficiency presents a “U” shaped curve that suppresses and then promotes. Industrial structure and the degree of openness have a positive influence, and urbanization have a negative influence on green development efficiency. Whereas, technological innovation has non-significant influence. Based on these findings, this paper proposes some targeted policy suggestions for promoting the green development efficiency.