Critical links have the characteristics of carrying large traffic flow and quickly affecting the operational performance of the road network. Existing regional traffic congestion coordination control methods do not consider the impact of critical links. To solve this issue, this paper proposes a regional traffic congestion coordination control method based on critical links. First, the median, gravitational index, and traffic sharing ratio are selected as the identification indexes of critical links in urban networks. Second, the road network vulnerability is assessed, and road link criticality is calculated based on joint entropy theory and multi-scale factor synthesis of multi-metric identification results. Then, the regional signal control range is determined, and a multi-stage signal control optimization model is developed. Finally, the optimal traffic signals for intersections are obtained by minimizing the pressure at the maximum phase of the road link and maximizing the capacity of critical links. To demonstrate the effectiveness of the proposed methods, two benchmarks (i.e., the MAXBAND method and existing traffic signals) are compared. The results show that (1) in terms of boundary control, the average vehicle delay at the boundary intersection of the road network is 34.62 s, an increase of 7.49 s and 5.03 s compared to the benchmark methods, respectively. (2) In terms of internal control, the average delay of the road network based on the proposed method is 87.54 s, which is reduced by 16.38 % and 28.73 % compared with the benchmark methods, and the queue lengths of the critical links are reduced by 21.47 % and 34.15 %, respectively. (3) The control process of the proposed method enables the number of vehicles within the road network to be maintained near the optimal carrying capacity, which gives the road network an efficient operating efficiency.