The rapid development of global transportation network and information communication technology has an important impact on regional economy and social spatial structure, and promotes the transformation of regional research paradigm. The coordinated development of urban agglomeration and regional functional linkage from the perspective of flow space has become an important issue in urban regional research. Different from the traditional central place theory that emphasizes the differences in scale and level of cities within the region, the flow space perspective helps to understand how the regional factor flow organizes cities of all scales and levels in the form of network with the background of space-time compression, and promotes the functional linkage and coordinated development within the region on the basis of reshaping the urban spatial relationship. Based on the literature review of relevant research at home and abroad, this paper constructs an analytical framework for the relationship between regional spatial factor flow and function collaboration, and discusses the regional function collaborative mechanism of urban agglomeration from three aspects: "how to reshape the regional spatial network by factor flow", "how to restructure the urban hierarchy by infrastructure connectivity" and "how to strengthen the regional functional linkage by functional complementarity". On this basis, taking the urban agglomeration of San Francisco Bay Area as an example, this paper discusses the evolution progress of San Francisco Bay Area from "single center agglomeration development" to "double-core symbiotic evolution", "polycentric development" and "generic network functional linkage development" from three aspects of liquidity, connectivity and complementarity. The study found that: 1) In the first stage (before the 1930s), fact flow strengthened the connection between San Francisco and Oakland, connectivity improved the status of Oakland, and functional complementarity promoted the symbiosis of the two cities. 2) In the second stage (1940s-1980s), the flow and converge of factors towards the south bay promoted the tripartite growth of San Francisco, Oakland and San Jose, transport connectivity strengthened the core-peripheral connection, and factor convection and functional reciprocity promoted the multi-center linkage development. 3) In the third stage (since 1980s), factor distribution and transportation network connectivity contributed to the generic network spatial structure, dislocation and complementary development strengthened the regional circulation and realized the functional linkage of the Bay Area. Based on the perspective of flow space, this paper reviews the basic situation of the development of world-class bay area urban agglomerations and excavates the internal mechanism of regional functional coordinated development driven by factor flow, which has reference significance for guiding China's cities from competition to competition and cooperation and establishing a new mechanism of regional coordinated development. The research shows that to promote the development of China's bay area in the future, we should: 1) Comply with the law of factor flow, innovate the mechanism and remove barriers to factor mobility, and promote the free flow of factors inside and outside the region; 2) Give play to the guiding role of the government and non-governmental organizations to improve the connectivity of software and hardware infrastructure within the region; 3) Explore the regional consultation mechanism, break through the regional administrative barriers, and formulate the regional development strategy of functional complementation and linkage with the help of multiple subject forces.