Abstract: Urban-rural factors have been the most important elements to promote urban-rural linkage and regional cooperation in an urban-rural community of destiny. Various social resources are very necessary for social production and business activities in urban and rural areas. Rural development has been hindered and slowed by the dual system of urban and rural areas in China over a long time. However, only a single flow has been considered in the urban-rural factors. The current relationship between urban and rural areas has shifted from separation to integration. The flow of urban and rural factors has been characterized by the "multi-factors two-way freedom flow", particularly with the national policies leaning toward rural development, and the implementation of national strategies, such as "new urbanization", "rural revitalization", and " integrated urban-rural development ". Furthermore, agricultural production has gradually brought into the various promises of ecological conservation, leisure experience, and cultural inheritance. Rural development has entered an accelerated transformation period. The rural pluralistic values can be expected to realize for the rural revitalization strategy and transformation. It is very necessary to clarify the influencing mechanism of urban-rural factor flow for the rural multi-values in the urban-rural integrated development and all-round rural revitalization. Taking Chongqing in South China as the research area, this study aims to evaluate the flow of urban and rural factors, as well as the realization of rural multi-values. A systematic analysis was implemented on the correlation between rural and urban factor flow and rural multi-values, in order to explore the influence mechanism of rural factor flow, and then to empower the rural multi-values realization and the path of realizing rural multi-values under the flow of urban and rural elements. The results showed that: 1) The correlation logic law was established between rural-urban factor flows and the realization of rural multi-values. The comprehensive effects of population mobility, resource transfer, and social interaction between urban and rural systems were utilized to realize the multiple values in rural areas. Among them, the core, key and driving forces were the population flow, the resource transfer, and the social interaction, respectively. 2) There was a significant spatial difference in the factor flows between urban and rural areas. The population flow was relatively frequent with a spatial pattern of "high in the west and low in the east". There was a small difference in resource transfer, the high integration degree of urban and rural areas, the more interaction between urban and rural systems, and the highly active degree of resource transfer. There was a large difference between urban and rural development in southeast Chongqing and northeast Chongqing. There was a low integration degree of urban and rural, and the low active degree of resource transfer. Social interaction was less with the low activity, indicating a spatial pattern of "low-value series and high-value flower arrangement". 3) Rural multi-values were represented by supply, regulation, inheritance, and service values. The realization degree of rural multi-values was normally distributed with a spatial pattern of "high in the south and low in the north, and flower arrangement in the north". The distribution of flower arrangement in the main metropolitan area was mainly in the middle and low-value areas, while the northeast and southeast of Chongqing were in the middle and high-value areas. Low-value area was less. 4) The rural multi-values were attributed to the comprehensive effects of multiple factors, such as population flow, resource transfer, and social interaction. Population flow shared a significant positive correlation with the supply and adjustment value with a positive promotion, whereas a significant negative correlation was found with the inheritance value with a reverse inhibition effect. Resource transfer presented a significant positive correlation with the supply, adjustment, and service value, indicating a positive promoting effect. Social interaction showed a significant positive correlation to the adjustment and service value with a positive promotion effect, whereas, a significant negative correlation was found in the inheritance value with a reverse inhibition effect. 5) Rural multi-values should be started from three aspects: a new urban-rural relationship with the county territory as an important carrier, in order to establish an institutional channel for the free flow of factors with the full factor flow as the core. The rural value can be expected to realize with the high quality and multi-values in modern agriculture.