The green economy has gained worldwide attention, especially in the urban agglomerations where population and economic activities are highly concentrated. However, what kind of urban agglomeration spatial structure is more conducive to promoting the green economy? No clear conclusions have been made. Here, we study the impact of urban agglomeration spatial structure on the green economy, and also reveal how urban agglomeration spatial structure influences the three subsystems of green economy. We find that: (1) urban agglomeration spatial structural evolution is closely related to green economy, while in the research period, most urban agglomerations are not located in the optimal range of the spatial structure that drives the green economy. (2) Towards polycentric spatial structure is contributive to green economic growth, however, the excessively polycentric could not benefit green economy. (3) The evolution of urban agglomeration spatial structure exerts heterogenous impacts on the three subsystems when green economy is decomposed into economic subsystem, resources subsystem, and environmental subsystem. Towards polycentric is more conducive to the improvement of economic subsystem and resource subsystem, while, the tendency to monocentric drives the environmental subsystem development. (4) Lastly, our conclusions enlighten the urban agglomeration development planning and spatial mode for approaching a better performance in green economy.