In the interconnection network operation of plug-in cross-line and post-station crossing, this paper considered the reasonable connection of cross-line train operation, and proposed a method based on coyote optimization algorithm (COA) to solve the train operation adjustment problem in the case of small-scale delay. Firstly, the connection relation of cross-line trains in “Y/T”-type cross-line operation is analyzed. Then, the optimization model is established with the goal of minimizing the total train delay time. Finally, the data of two “Y”-type subway lines in a city are simulated to verify the effectiveness and rapidity of COA in solving the adjustment model, and it is necessary to choose different connections to adjust the delay of different scales. COA achieved better results than IPSO and the computing time was less than 10s, which met the time requirements.