Based on the urban-rural equivalence, the Global Principal Component Analysis (GPCA) method is used to measure the China's urban-rural multi-dimensional integration levels, and the Global and Local Moran Index, Local Getis-Ord G_i^* Index are performed to reveal the spatial distribution of urban-rural multi-dimensional integration levels in China during 2000-2016. And finally, the spatial econometric model is introduced to explore the influencing factors of urban-rural integration development from the aspects of labors, land, capitals and industries. Research findings are as follows: (1) the trend of urban-rural integration development in China is well and orderly, but has regional heterogeneity. The agglomeration effect is obvious in Eastern China, and the social and economic coordination level has always occupied the first and the second places. (2) China's urban-rural multi-dimensional integration levels often show spatial autocorrelation. The HH values of urban-rural integration overall level are concentrated in Central China and Eastern China, while the LL values are gathered in Western China. The hot and cold spots are located to the southeast and northwest of Heihe-Tengchong Line, respectively. Also the high values of economic integration have always corresponded to those of ecological and environmental integration. Population integration level decreases from Eastern to Western China. Spatial integration level presents the "core-edge" structure such as Beijing, Shanghai and Guangdong. Spatial spillover effect of the economic integration development is obvious in the coastal region of China, while the development of ecological environment integration and economic integration has spatial dislocation. And the clusters of social integration high values are in Central China. (3) The ways of the urban-rural multi-dimensional integration are as follows: Firstly, we should improve the quality of rural labor forces and promote the interaction between urban and rural residents. Secondly, we should stimulate the multi-function of rural land and control the disorderly urban expansion. Thirdly, we should take financial expenditures in a reasonable range and provide a perfect financial support in urban and rural areas. Finally, industrial restructuring is also needed. And moreover, regulating the behavior of the local governments will be benefit to the urban-rural multi-dimensional integration and good governance in China.