Urban agglomerations (UAs) in China play a vital role in the distribution of productive forces and constitute the most dynamic and potentially rich core areas for future economic development. However, the rapid economic growth and high-intensity interactions seen in relation to these areas, results of the high population densities and aggregation of industries in UAs, also pose significant ecological threats to the environment. This paper attempts to analyse changing trends in the input–output efficiency of UAs in China based on the data envelopment analysis (DEA) approach. The paper investigates the DEA efficiency of UAs with different population sizes and geographical locations, explores the relationship between the elements that make up a decomposed model of efficiency and compares the efficiency performance of China’s UAs with that of 35 central cities. Moreover, the exogenous factors determining the input–output efficiency of UAs, the question of how to improve UAs’ efficiency performance, as well as the focus of future research are also discussed. A number of valuable implications have been drawn from the study, which may be helpful to the task of understanding more deeply the high-density aggregation effects of UAs in China.