The use of multi-perspective and multi-scalar city networks has gradually developed into a range of critical approaches to understand spatial interactions and linkages. In particular, road linkages represent key characteristics of spatial dependence and distance decay, and are of great significance in depicting spatial relationships at the regional scale. Therefore, based on highway passenger flow data between prefecture-level administrative units, this paper attempted to identify the functional structures and regional impacts of city networks in China, and to further explore the spatial organization patterns of the existing functional regions, aiming to deepen our understanding of city network structures and to provide new cognitive perspectives for ongoing research. The research results lead to four key conclusions. First, city networks that are based on highway flows exhibit strong spatial dependence and hierarchical characteristics, to a large extent spatially coupled with the distributions of major megaregions in China. These phenomena are a reflection of spatial relationships at regional scales as well as core-periphery structure. Second, 19 communities that belong to an important type of spatial configuration are identified through community detection algorithm, and we suggest they are correspondingly urban economic regions within urban China. Their spatial metaphors include the administrative region economy, spatial spillover effects of megaregions, and core-periphery structure. Third, each community possesses a specific city network system and exhibits strong spatial dependence and various spatial organization patterns. Regional patterns have emerged as the result of multi-level, dynamic, and networked characteristics. Fourth, adopting a morphology-based perspective, the regional city network systems can be basically divided into monocentric, dual-nuclei, polycentric, and low-level equilibration spatial structures, while most are developing monocentrically.