With the improvement of urbanization and the development of urban clusters, optimizing the spatial structure of urban system has become important power in releasing the potential regional efficiency in China. After combing through academic history, it could be found that there are obvious differences in the spatial structure efficiency among urban systems in different countries or locations. Therefore, it is not clear whether single-center or multi-center structure is more conducive to efficiency improvement. However, with continuous spatial structure evolution, it is inaccurate to statically evaluate the efficiency of the urban system structure without the process of dynamic adjustment of industrial firms. The reason lies in that for the area where the industry is net outflow, no matter what the spatial structure, the probability of efficiency loss is higher. This paper innovatively integrates the process of firms’ entry and exit into the construction of urban agglomeration indicator, and measures the urban productivity on the basis of recalculating the depreciation rate and capital stock, so as to use the spatial econometric model to test the theoretical mechanism that affects the spatial efficiency of the urban system. It is found that the multi-center urban system structure is more conducive to the improvement of regional productivity, which needs to be integrated into the process of dynamic industrial agglomeration. This result further shows that ignoring the process of firms’ entry and exit may lead to biased results and lack of explanatory power. Meanwhile, the urban scale efficiency has been significantly improved, while it is not conducive to the improvement of technological progress and technological efficiency. It is also found that the polycentric features of the Beijing-Tianjin-Hebei and the urban agglomeration in the middle reaches of the Yangtze River are weak, which needs spatial efficiency improvement. In contrast, the multi-center structure and industrial agglomeration of the Yangtze River Delta and Pearl River Delta urban agglomerations have performed better synergy effect. In addition, industries may be dynamically adjusted within the urban system, resulting in an uneven distribution of productivity among cities. Further research shows that the polycentric structure and industrial dynamic agglomeration are conducive to the coordination of urban productivity. However, it is also found that it is more conducive to the efficiency improvement of large-scale cities, but restricts the development of small cities, which alludes to the fact that in the process of multi-center structure forming, large-scale cities are still the biggest takers of benefits. Although the spatial measurement model could weaken the endogenous effect, this paper uses urban surface roughness and regional river density as the instrumental variables of industrial agglomeration and urban system structure referring to the existing research, so as to reduce the empirical bias. The result shows no fundamental change. This paper also uses the adjusted Herfindahl-Hirschman Index, the transforming primacy index and the per capita GDP to conduct robustness tests to enhance the credibility of the conclusions. The results of the influence mechanism test show that the process of dynamic industrial agglomeration among cities has accelerated the polycentric urban system, and the process of market integration has effectively released the spatial efficiency of the multi-center city system. Therefore, it is necessary to deepen the coupling and synergy relation between the urban system and the dynamic agglomeration of industries, meanwhile to promote market integration to further release the potential efficiency. At the same time, while highlighting the dominant position of central cities, it also needs to pay more attention to coordinated development of small and medium-sized cities, and to build a virtuous circle system within the urban agglomerations under the framework of dual-circulation development in China.