The rapid expansion of large cities in China has substantially increased energy consumption. With ever stringent environmental policy in force, energy efficiency becomes an important issue. As the emergence of these urban agglomerations (UAs) is usually due to externality effects of spatially concentrated factors, this paper investigates how these factors can affect energy efficiency. Based on mono index, which is used to describe the spatial location information, we have constructed the spatial-structure index of UAs. Using panel data on ten major UAs in China from 2008 to 2017, we find that, in the whole sample, there is an inverse relationship between the spatial structure of UAs and energy efficiency: The higher the concentration degree of factors of UAs, the lower the energy efficiency. Across different regions, however, the relationship between spatial structure and energy efficiency is heterogeneous. The concentration degree of factors in the eastern and central regions of China is relatively high, and the spatial structure there does lead to a decrease in energy efficiency. By contrast, UAs in China’s western region are in a period of factor concentration, with spatial structure playing, in that region, a positive role in improving energy efficiency.