Developing new types of transportation is considered a key solution to meet the extreme demands placed on traditional transportation infrastructure due to the increasing flow of production factors for national urban growth, especially in emerging economies. Both city transportation networks and city economic networks reflect intercity relationships in urban systems from different aspects. Although HSR networks are being developed rapidly worldwide, we still lack a deep understanding on how HSR relates to the economic growth of urban agglomerations from a “double-network” perspective. In this research, we first built city HSR networks and city economic networks, respectively, before the QAP method was used to examine their relationship during 2010–2015. By analyzing comparatively the differences of the coupling relationship in various areas in China as a typical case, this study contributes to the understanding of the dynamic coupling relationship between new forms of transportation and regional economic development. We found a strong coupling relationship between HSR and economic growth, and HSR tends to play a more prominent role in promoting urban integration and development in areas with more developed economies (coefficients of more developed areas are all above 0.6, while that of less developed areas are below 0.4). Such correlated relationship is more obvious in smaller administrative scopes compared to cross-administrative regions. This study proposed a research framework for “double-network” analysis in exploring the relationship between the different networks. It could also provide policy implantation for balanced regional development in emerging economies. •A new approach is provided to study the relationship between city transportation and economy system.•Network comparative analysis of city high-speed rail network and city economic network in China•Urban spatial patterns highly correlate with regional economic structure.•A significant positive coupling relationship exists between high-speed rail and economic growth.•Positive relationship between new form of transportation and economic growth is more obvious in developed areas.