At the fifth meeting of the Central Financial and Economic Committee of the Communist Party of China in August 2019, it is emphasized that central cities and urban agglomerations are becoming the main spatial forms that carry development elements. Under the new situation, it is necessary to promote coordinated regional development and create a balance in development. At present, the regional economic development orientation of increasing the primacy of cities and strengthening the role of central cities in various regions of China with economic development as the core goal will lead to the formation of the siphon effect of the central city on the surrounding areas, deteriorating the coordinated development of the region, or will it form a stronger leading role, expand its radiation diffusion range, and narrow the development gap within the region? The research aims to analyze the important spatial form of China at this stage, the urban agglomeration, and the impact of the change of the central city’s primacy on the overall economic growth and coordinated development of the region. At the theoretical level, the study analyzes the agglomeration and diffusion effects of central cities and the mechanism of coordinated regional development based on the theory of regional non-equilibrium development and the inverted U-shaped model of optimal urban scale, and constructs a mechanism for the formation of the central city’s primacy on the coordinated development of regional economy. The theoretical framework includes three aspects: the inhibitory effect of the central city on the coordinated development of the region under the agglomeration effect, the promotion effect of the central city on the coordinated development of the region under the diffusion effect, and the mechanism of the different primacy levels of the central city. The changes in different stages of regional economic development and their internal mechanism are analyzed. At the empirical level, the study takes the nineteen major urban agglomerations in China as the research object, uses the panel data of the nineteen major urban agglomerations in China from 2006 to 2017 to carry out fixed effects analysis, and controls the endogeneity problem of the model through the endogeneity test. In order to further explore the nonlinear effect of the central city primacy on the coordinated development of the regional economy, the study further analyzes the effect of the central city primacy on the regional economic coordination through the interaction model of the government’s strategic planning guidance and regional institutional policies, and the identification of the central city primacy distribution. The impact of development and the impact of government strategic planning, regional institutions. The study found that: First, the primacy of central cities has an inverted U-shaped effect on economic growth. Second, the primacy of the central city has a positive U-shaped effect on the coordinated development of the regional economy. Third, the emergence of the national central city policy will further promote the siphon effect of central cities. Although the administrative division does not affect the overall economic growth of the urban agglomeration, it will lead to the widening of the development gap between different provinces within the urban agglomeration. Fourth, urban agglomerations that are still being cultivated and immature in the central and western regions of China should focus on the construction and development of sub-center cities and small and medium-sized cities, and promote the formation of a gradient urban agglomeration structure system in the region.