The evaluation of green economic efficiency is of great significance for evaluating the green development quality and economic transformation effect of resource-based cities in arid regions. This study built an input-output index system based on green development level and used the SBM-Undesirable and Malmquist-Luenberger index models to decompose the static efficiency and dynamic efficiency of 20 resource-based cities in the arid region of China from 2006 to 2016. It also examined the differences in green economic efficiency based on life cycle and functional classifications and dynamic change types and summarized the green development level and characteristics over 11 years for these resource-based cities. The results show that: (1) The static efficiency of green economy of these resource-based cities is generally at a low level (0.932), and the efficiency value between cities is quite different, Luliang, Yan’an and Qingyang have experienced high level of green development. (2) Classified by functional types, green economic efficiency pattern of these cities shows the following characteristics: petroleum (0.995) > comprehensive (0.958) > metal (0.908) > coal (0.904). The trends of change of metal- and coal-mining cities are similar and green economic efficiency in both types of cities is at a low level. Classified by life cycle types, the result shows that: growth type (0.978) > regeneration type (0.945) > maturity type (0.920) > decline type (0.882), while the green development of decline type cities is clearly lagging behind obviously. (3) The dynamic efficiency of green economy of resource-based cities in arid areas of China was generally in a state of growth, which gradually rose, then rapidly rose, and then slowly rose. (4) According to the ML index, the green economic efficiency state of cities is divided into four types, among which growth and fluctuating growth types account for 65%. Datong, Baotou, and Baiyin cities have higher dynamic efficiency values,and have faster growth rate of green economy. On the whole, under the guidance and overall management of national policies, the green development level of resource-based cities in arid areas is gradually improved.