Strategic emerging industries are key areas to promote industrial restructuring in China. Simultaneously, the government is focusing on the green economy for economic development. However, few studies have discussed the influence of strategic emerging industrial agglomeration on green economic efficiency. This study fills this gap based on the theory of location entropy and the super SBM model considering a non-expected output. A spatial Durbin model is introduced, and panel data of 30 provinces in China from 2012 to 2016 are selected to test the spatial spillover effect of strategic emerging industries on green economic efficiency. We found that: (1) China’s overall strategic geographical spatial agglomeration shows a weakening trend from east to west, which is consistent with regional economic development, (2) green economic efficiency in most regions is below the forefront of production and economic, technological and labour input, (3) the direct effect of strategic emerging industrial agglomeration on green economic efficiency is significantly positive, the indirect effect is not significant, and the total effect is significantly positive, and (4) the direct, indirect, and total effects of economic development level, industrial structure, energy structure, foreign direct investment, and urbanization level on green economic efficiency are different.