Based on the European Control (EC) estimation model and using aircraft configuration ratio and flight stages as impact parameters, this study estimated the time delay cost and the total time delay cost of Chinese hub airports in 24 hours with the improved EC estimation model. Then the air routes effect of time delay cost was analyzed and a comparison with the United States was carried out. The conclusions are as follows: 1) Time delay cost of the compound hub airports is generally higher than that of the regional hub airports while per minute delay cost and gating cost of regional hub airports are higher. This is caused by the centrality of the network structure of air routes, the need of aero geographic market, and the influence on the transmission efficiency of the aviation network in China. The air maintenance cost of hub airports accounts for the largest proportion of the total cost of time delay, which indicates that there are defects in the configuration of air corridors in China. 2) The spatial heterogeneity of the total cost of time delay between hub airports (air routes) and hub airport to non-hub airport (air routes) is caused by air route attributes, which are determined by the joint action of geographic market demand and the location of participating airports in air-corridors in the sky. The specific performance is affected by the difference of clustering levels: the hub and non-hub airports (air routes) generally exist in the low level, and the hub airports (air routes) basically exist in the high level. There is a significant difference in the total cost of time delay between the compound hub airports and the regional hub airports. The three routes in the fifth level clustering connect PEK, SHA, CAN, which is dominated by the aero geographic market, and the total cost of time delay accounts for 9.22% of the total cost of all routes in 24 hours. Among the total cost of time delay between hub airport and non-hub airport (air routes), PEK-SZX is the highest, followed by SHA-NKG. 3) The difference in time delay cost of hub airports and air routes between China and the United States is mainly manifested in the different proportion of the flight stages, which is determined by the width of characteristic path and the number of track intersections in air corridors in the sky.