Concerning the problem that intercity train operation plans fail to match urban rail transit capacity effectively, an optimization method of intercity train operation plan considering regional coordination was proposed. Firstly, the minimum passenger travel cost and maximal benefit of railway department were considered as the optimization objectives, the transport capacity of intercity train, traffic demand between origins and destinations and carrying capacity were considered as constraints of this model. Secondly, the matching degree limit of transportation capacity was considered, a multi-objective nonlinear programming model of intercity train operation plan considering regional coordination was constructed and an improved simulated annealing algorithm was designed to solve the model. Finally, the Guangzhou-Shenzhen intercity railway was taken as an example to make two pairs of comparative analyses. The experimental results show that the train operation plan considering the regional coordination makes the total travel cost of passengers reduced by 4.06%, the railway department revenue increased by 9.58%, the total cost of passengers and railway system decreased by 23.27%. Compared with genetic algorithm, the improved simulated annealing algorithm is better in solving quality and convergence speed. The proposed model and algorithm can give full consideration to the interests of both passengers and railway department, and provide an effective solution for the optimization of intercity train operation plan.