The green level of urban agglomeration in the upper reaches of the Yangtze River is directly related to the high-quality development of the Yangtze River Economic Belt. The understanding of green development efficiency law of urban agglomeration in the upper reaches of the Yangtze River is the basis of its choice of high-quality development path. Based on the relevant data from 2009 to 2018, DEA method and Malmquist index model are used to evaluate the static and dynamic performance of 23 cities in the three urban agglomerations of the upper reaches of the Yangtze River. The results show that: (1) From the temporal dimension, the green development efficiency of urban agglomerations in the upper reaches of the Yangtze River presents an obvious “down-up-decline” overall evolution characteristic. (2) From the spatial dimension, the green development efficiency of Chengdu-Chongqing, central Guizhou and central Yunnan urban agglomerations shows the hierarchical structure difference of “national urban agglomeration > regional urban agglomeration”. (3) The green development efficiency of central city does not match the level of its economic development. (4) The equilibrium degree within the urban agglomeration presents a certain difference. Strengthening technological innovation development, regional coordinated development and green transformation development of central cities are important ways to improve the green transformation development of urban agglomerations in the upper reaches of the Yangtze River.