With the rapid development of communication and transportation technologies, the urban area is increasingly becoming an ever more dynamic, comprehensive, and complex system. Meanwhile, functional polycentricity as a distinctive feature has been characterizing urban areas around the world. However, the spatial structure of the urban area has yet to be fully comprehended from a dynamic perspective, and understanding the spatial organization of polycentric urban regions (PUR) is crucial for issues related to urban planning, traffic control, and urban risk management. The analysis of polycentricity strongly depends on the spatial scale. In order to identify functional polycentricity at the intra-unban scale, this paper presents a traffic flow-embedded and topic modeling-based methodology framework. This framework was evaluated on real-world datasets from the Wujiang district, Suzhou, China, which contains 151,419 records of taxi trajectory data and 86,036 records of points of interest (POI) data. This paper provides a novel approach to examining urban functional polycentricity via combining urban function distribution and spatial interactions. This proposed methodology can help urban authorities better understand urban dynamics in terms of function distribution and internal connectedness and facilitate urban development in terms of urban planning and traffic control.