Abstract: The bi-directional flow and rational allocation of urban and rural resources can surely become a powerful support to promote the coordinated development of urban agriculture (UA). UA in large and medium cities will also play an important role in promoting the integration of urban and rural areas. Based on the field survey data of UA in Chongqing, Guiyang and Wuhan, this paper summarized and analyzed the operation modes and the innovative and rational allocation of urban and rural resources to drive the development of UA from the perspective of urban-rural integrated factor flow, and identified the growth point and potential for UA and modern agriculture. This paper also explored the obstacles to the development of UA. Results show that the typical modes of urban agriculture development driven by the rational allocation of urban and rural resources in large and medium-sized cities in central and western China are mainly divided into five types: capital resource, labor resource, infrastructure resource, information and technology resource, and rural collective assets reform driven. Different modes have differences in connotations, basic elements and application conditions. Rational allocation of urban and rural resources drives the development of UA, which can not be separated from the government’s support and the promotion of the integration of three industries. However, the current development of UA still has obvious homogeneity trend, low participation rate of farmers, difficult implementation of specific policies at the grass-root level, and lack of transformation and upgrading elements and other development. Therefore, to promote the sustainable development of UA, this paper suggests to formulate scientific and rational planning, to strengthen the consciousness of farmers, to deepen the reform of agriculture and rural areas, to pay more attention to the continuity of policies, and to enhance the flow channels of resources.