To restructure the evaluation index system of urban and rural integration from population, space, economy, society and ecological environment, the dynamic coupling coordination model was selected to measure the urban and rural multi-dimensional integration level, and the global Moran index and the local indicators of spatial association (LISA) were used to reveal the spatial distribution characteristics of the urban-rural multi-dimensional integration level in Huaihai Economic Zone. And then, the spatial correlation pattern in the study area was analyzed by the spatial structure index (SSI) from the population flow, logistics flow, capital flow and information flow. And finally, the driving mechanisms of urban-rural integration in the study area were explored by the fixed effect spatial error model (SEM-FE) from the perspective of these four types of flow. The results are as follows: (1) The urban-rural multi-dimensional integration levels are low but go well, the overall level in the research area rose from 0.016 in 2003 to 0.028 in 2017, with an annual rate of 0.08%. When the urban-rural multidimensional integration structure maintains stable in the research period, the economic integration is the highest, while the spatial integration is the lowest. (2) The regional interrelation is close in the context of population flow and capital flow, while it shows a "core-periphery" structure under the material flow and information flow. In general, the spatial structure in Huaihai Economic Zone is a decentralized network with multiple central cities, which lays a good foundation for the future development of urban-rural integration and inter-regional coordinated development. (3) In order to achieve the improvement of quantity and quality of urban-rural integration in Huaihai Economic Zone, we should shift the effect of the core area from agglomeration to diffusion, and need reasonable labor distribution and trading to stimulate the regional comparative advantage fully of each city node. Moreover, it is necessary to assist a series of cultural, economic and political systems in the implementation of local and national policies, because urban and rural integration development is a big cycle system of the socio-economy.