With the enormous radiation range, great potential and vigor, urban agglomerations are deemed as the core growth pole both at present and in the future under the background of globalization and new-type urbanization in China. Behind the seemingly ever-growing urban agglomerations, however, massive input elements such as resource, labor, capital, and other factors are needed. It is of profound significance to evaluate the economic performance of urban agglomerations, which may vigorously promote the sustainable and healthy development of urbanization. How to objectively evaluate the efficiencies such as industry scale concentration, resource allocation, and technological change of urban agglomerations has become an important question. Therefore, in this study we applied the data envelopment analysis (DEA) model to quantitatively measure the input and output efficiency of typical urban agglomerations in China from 2000 to 2013, based on time series data including capital input, urban construction land increment, labor supply, scientific-technological investment, and economic output value. Moreover, we analyzed urban agglomerations' total factor productivity index (TFP) dynamically by means of Malmquist productivity index method and lucubrated their spatial and temporal differentiation patterns, mechanisms of change, influencing factors, and other related contents. The results show that the urban agglomerations' stationery cross-section input and output efficiency made significant strides but an unbalanced spatial distribution pattern remained. In 2000, the average comprehensive technological efficiency was only 73.1% of the optimal level with barely three large urban agglomerations achieved the optimal DEA efficiency. After years of steady development, the corresponding index reached 96.8% of the optimal level with eight urban agglomerations achieved the optimal DEA efficiency. However, from the perspective of dynamic time series analysis, urban agglomerations' TFP decreased by 6% from 2000 to 2013 mainly due to the poor performance of technology change index. Unlike the disappointing performance of technology change index, other indices such as comprehensive technological efficiency change index, pure technological efficiency change index, and scale efficiency change index all shaped up, indicating that the level of resource allocation and utilization efficiency rose steadily during this period. The lag of the contribution of technological progress to a certain extent offset the positive effects brought by the expansion of urban agglomeration and the optimization of resource allocation. Specifically, only the Yangtze River Delta, the Pearl River Delta, and Beijing-Tianjin-Hebei urban agglomerations gained ascending contribution of technological progress, which illustrates that the current development stages and dynamic mechanisms of urban agglomerations in China maintained diversified characteristics. To conclude, this article puts forward a series of specific suggestions to optimize the development of urban agglomerations in China, namely, moderately expanding the scale of urban agglomerations, placing emphasis on input and output efficiency leaning against technological changes and transforming the present unbalanced regional development situation.