To enhance the knowledge of structural differences between high-speed rail (HSR) and air transport (AT) networks, topological characteristics of the two networks are compared in terms of network compactness, node importance, connection heterogeneity and network hierarchy. Social network analysis methods and schedule data of 2019 were used in this study. The results show that similar characteristic path length and clustering coefficient are presented in the two networks, and network density and compactness of HSR network are larger. On average, node connectivity in HSR network is higher, while bridging roles and global accessibility of nodes in AT network are better. Stronger heterogeneity can be found in the distribution of train flow in HSR network compared with distribution of flight flow in AT network. Train flow in HSR network are mainly distributed in east-east, east-center, center-center regions, while flight flow in AT network are mainly distributed in east-east, east-center, east-west regions. The proportion of train flow related to the bridge layer in HSR network is higher, while the proportion of flight flow related to the bridge and periphery layers in AT network is higher.