Megaregions are the new engines of global and regional economic growth, and they often are considered a principal urbanization platform in China. To understand megaregional processes’ responses to China’s regional policies, this study focused on two aspects of integration development in the Central Yangtze River megaregion between 2000 and 2014: The internal collaborative networks using enterprises’ headquarters-branch locations as a proxy measurement and the role of regional transportation in the integration networks. Based on a three-step network analysis, the Central Yangtze River megaregion was increasingly similar to a polycentric urban system with Wuhan, Changsha, and Nanchang as the dominant service cities, and there were some indications of a preliminary urban network formation. However, integration development remained a government-led administrative process with administrative boundaries that significantly influenced the network structure. A panel regression analysis further suggested that transportation accessibility to the three central cities was the key determinant of network participation for the peripheral cities compared to economic performance. This work contributes to the debate on the hierarchical-administrative properties of China’s megaregions and transportation implications of the economic integration process.