Network-wide traffic control strategies (e.g. perimeter control and route guidance) in urban networks have recently been mainly studied to relieve or postpone congestion based on the theory of macroscopic fundamental diagram (MFD). Nevertheless, these studies are mostly applied to the statically partitioned networks or the dynamic networks that fail to fully consider traffic state prediction, conflicting with strongly spatiotemporal variability of traffic congestion or objective of active traffic management (ATM). This paper proposes a methodology to dynamically identify critical congestion warning areas from heterogeneous urban road networks, which aids to design efficient perimeter control approaches. In the methodology, a dynamic directed weighted network is built on the base of the link connectivity and the real-time traffic loads, and a link travel time prediction method based on Kalman filter is developed to calibrate directed weight values and undirected input values for links. With the undirected link input information, a dynamic congestion warning community detection method which consists of three consecutive steps is developed. Firstly, it could capture emergence of new congestion areas based on the definition of congestion seed intersection. Secondly, expansion and regression of each congested area could be achieved with the objectives of spatial compactness and traffic condition homogeneity. Thirdly, a two-level merging algorithm of adjacent different congestion areas is designed utilizing modularity model in community detection of complex networks. The proposed methodology is validated using ground truth data from downtown network of Jinan City in China. The results show that the proposed algorithms can efficiently track congestion evolutionary processes and effectively detect congestion warning areas from the test real network.