In the era of digital economy, the widespread application and promotion of data elements and digital technology breaks the physical barriers of time and space, promotes inter-city division of labor and collaboration, profoundly reshapes the regional economic and geographical pattern represented by urban agglomerations, and accelerates the evolution of the spatial system of urban agglomerations from the traditional scale and hierarchy order to the new era of balanced development mode. At the same time, the interactive connection of multiple factors flows within urban agglomerations promotes the formation of networked spatial structure, effectively improves the overall network externality, and further strengthens the enabling performance of the digital economic development level of urban agglomerations in improving the spatial system balance. Therefore, the internal mechanism of digital economy enabling the balanced development of urban agglomerations' spatial system has both direct effects and the moderating effects of various flow networks in urban agglomerations from the perspective of flow space, including traffic information network, traditional factor network and innovation factor network. Under the guidance of the theoretical framework, this paper takes 19 urban agglomerations in China as samples, establishes a multi-source database, measures the digital economic development index, the degree of spatial system balance and the network externality based on three kinds of flows, summarizes the characteristic facts, and carries out empirical tests. The analysis based on the characteristic facts shows that the digital economy level of 19 urban agglomerations in China has been steadily improved, but there is a large regional development gap, forming a relative gradient development pattern. The spatial system of most urban agglomerations is more balanced, while a few urban agglomerations show a trend of polarization. Each urban agglomeration has formed a certain network-type spatial structure, but there exists heterogeneity between individuals and regions. The analysis based on empirical tests shows that the digital economy of urban agglomerations directly improves the degree of spatial system balance, and the results remain robust after the regression of instrumental variables and the replacement of core explanatory variables. At the present stage, the flow of goods is more conducive to the spatial distribution of economic activities than the flow of people, and the regional industrial structure dominated by the tertiary industry accelerates the spatial polarization of urban agglomerations to a certain extent. The formation and development of transportation information network, traditional factor network and innovation factor network in urban agglomerations have a positive moderating effect, that is, to further strengthen the empowerment performance of digital economy to improve the degree of spatial system balance in urban agglomerations. The regression results of the direct effect of urban agglomerations in the eastern, central and western regions of China are basically consistent, but there is a large regional heterogeneity in the moderating effect. This paper firstly establishes the theoretical mechanism framework of digital economy promoting the balanced development of urban agglomeration spatial system, and demonstrates it through the methods of characteristic fact interpretation and empirical test analysis, which provides reference and reference for in-depth understanding of the reform direction and optimization path of urban agglomeration spatial system in the digital economy era, and has certain enlightenment for promoting the high-quality development of urban agglomeration in China.