The origin, spatial pattern, and evolution of urban system have been hot research issues in the field of urban system. In this study, the theory of “urban tree (UT)” was proposed to address these issues. The spatial pattern of urban system can be expressed by the phrase UT and the growth of the UT reflects the origin, spatial pattern, and evolution of urban system. Analysis of the UT growth can reveal the evolutionary mechanisms of the urban system. We present an UT resistance model to determine spatial extension in the evolutionary processes of urban system. The Thiessen polygon method and spatial remapping were used to construct the UT. Data collected in 1995, 2000, 2005 and 2010 from cities in the Huai River Basin were used to construct the UT model to analyze the origin, spatial pattern, and evolution of urban system in this region. Xuzhou City was the UT “tree root” and the UT growth the followed four paths. Growth of cities on the nodes of these paths promoted the evolution of urban system. The UT theory expresses the spatial pattern and evolution of urban system in an intuitive way and helps to explain the origin and evolution mechanisms of urban system. Empirical research supported the UT theory. Because of the operational and visual expression, this theory has broad application prospects in the urban system research.