The relationship between air cargo transportation development and the spatial structure in urban system is an important research field in air transportation. Based on the data of the airport cargo transportation and the airline network from 1980 to 2008, the air cargo spatial pattern is illustrated. Due to the improvement in aviation service and the expansion of air transport network, the linkages between domestic cities were gradually enhanced. According to the research, the air cargo flow was changing the spatial interaction. First, the air cargo flow attenuated with the inter-city distance. About 85% of the domestic air cargo flow took place between the cities where the inter-city distance ranged from 1000 km to 2000 km. Second, the "Hub-and-Spoke" network was found shaped basically. In the domestic cargo network, Beijing, Guangzhou and Shanghai were the three large national hubs, and Kunming, Chongqing and Urumqi were three large local hubs. Last, the mega cities controlled the air cargo network, which made the cargo flow agglomerate into a few cities. Therefore it is important to design airline network as a "Hub-and-Spoke" structure, which should conform to the social and economic development of the regions. The hubs should be located in the central and west China, and the linkages should be strengthened between the west air cargo hub and the west medium and small airports. A rational air cargo transport network should be adapted to the city system in China as well to guide the local economy’s continuous growth in both quantity and quality.