Different period remote sensing images of three years in 2000, 2010 and 2019 were selected as the data source, and the cost weighted distance model and urban-rural potential index were used to express the spatial connection. Besides, urban-rural expansion intensity index and urban-rural expansion speed index were also used to analyze urban and rural spatial structure of Shiyang River Basin. GIS technology combined with road grade and length was used to calculate the shortest time distance between urban and rural nods. Spatial association and interaction between urban and rural systems were analyzed through the time and distance, and the spatial structure changes and influential patterns of the Shiyang River Basin were discussed. The results showed that: (1) the urban-rural spatial expansion was dominated by central cities, the small towns had cluster distribution while the large towns were scattering. The urban-rural spatial structure system showed Jinchang, Wuwei city were the axis points, and Yongchang, GuLang, Minqin and Tianzhu are the axis line, which formed pointaxis structure and the “F” layout. (2) The pattern of city-county-town showed network development patterns, which indicated the influence of administration privilege to the spatial structure of urban-rural system. The key connection between the urban and rural area was road network but the administrative association was the dominated factor, especially inside of the whole river basin. (3) The administrative contact was much more than economic contact, management contact and information exchanges. The spatial structure and system formed a three-level management network pattern that was “city-county-small town” in Shiyang River Basin.