The prominent contradiction between passenger demand and capacity in rush hours at subway stations causes inconveniences to travel and even leads to safety risks. Existing research on the cooperative control of passenger flow at stations mostly focuses on a single direction, rarely considering transfer passenger flow control. This study formulated a coordinated dynamic control strategy for multiple stations in both directions as a deterministic mathematical programming model to optimise the crowded passenger flow. The optimisation objectives were set as the warning levels of crowded passenger flow and the detention time of all passengers. The constraints included limitations on station service capacity, train capacity, and the number of people boarding trains. Additionally, considering separate control over the transfer inbound passenger flow at transfer stations, an upward- and downward-direction coordinated dynamic control model was constructed. Numerical experiments based on real-world data from the Nanjing Metro Line 1 were conducted to investigate the effectiveness of the proposed cooperative control scheme and evaluate its performance.