On the basis of summarizing the dynamic mechanism research of the interaction between urban-rural dual system both home and abroad, the article introduces non-linear dynamic model of urban-rural coupling region's system according to modern scientific theories, and extracts coupling degree index so as to reflect the evolution of the whole system and the level of coordination between the urban dominant correlative system and the rural one. Taking Nanjing city as an example, the method of principal component analysis is used to pick up four components among 28 indexes (namely, economic development, social coordination degree, resource allocation rate, and the negative environmental feedback mechanism) that could be undertaken demonstration analysis in terms of coupling degree, and to get the knowledge of evolution discipline in terms of Nanjing's urban-rural coupling region's system. This paper provids theoretical foundation for scientific planning and managing the region in term of how to recognize the coupling discipline of the urban-rural coupling regions system, how to find out the dominant factors and its functions of the urban-rural coupling region system evolution, and how to choose the new regional development patterns and coordinate new relationship between the urban and the rural system. Due to the urgent need of land and other basic infrastructures for central city's further development, Nanjing's urban-rural coupling region expands rapidly and inevitably becomes impediment to cooperative development between the urban and the rural. Under the circumstance that the urban and rural areas are highly coupled, the pressing task is to hold the whole system and its evolution trend related to the main associated system both the urban and the rural. The relationship of the above mentioned systems and the state of the whole system should be defined so that the whole system could be evaluated. Consequently, the proper measures for development can be adopted and the evolution speed of the main associated system both the urban and the rural can be regulated to realize harmonious development of the urban-rural coupling region system.