Urban-rural integration focuses on the exchange and integration of the factors such as population, technology, capital, resources and so on but does not exclude the difference,on the contrary,the difference between urban and rural areas is the basic dynamic power for the cooperation and exchange between urban and rural areas and for promoting coordinative development with each characteristic under scientific and rational deployment. The research finds that ,in the process of urban-rural integration at upper reaches of Yangtze River,Chongqing and Sichuan march at the head of Yunnan and Guizhou,furthermore,the urban-rural integration level of Chongqing and Sichuan is 56.41 percent and 42.85 percent respectively and reaches middle and high level.