Recently, virtual coupling has aroused increasing interest in regard to achieving flexible and on-demand train operations. However, one of the main challenges in increasing the throughput of a train network is to couple trains quickly at junctions. Pre-programmed train operation strategies cause trains to decelerate or stop at junctions. Such strategies can reduce the coupling efficiency or even cause trains to fail to reach coupled status. To fill this critical gap, this paper proposes a cooperative game model to represent train coupling at junctions and adopts the Shapley theorem to solve the formulated game. Due to the discrete and high-dimensional characteristics of the model, the optimal solution method is non-convex and is difficult to solve in a reasonable amount of time. To find optimal operation strategies for large-scale models in a reasonable amount of time, we propose an improved particle swarm optimization algorithm by introducing self-adaptive parameters and a mutation method. This paper compares the strategy for train coupling at junctions generated by the proposed method with two naive strategies and unimproved particle swarm optimization. The results show that the operation time was reduced by using the proposed cooperative game-based optimization approach.