To improve the operational service of urban rail transit Y-type lines, a method for optimizing the train schedule under the flexible train composition mode with online coupling/decoupling is proposed. Initially, a unique flexible train composition scenario specifically designed for Y-shaped lines is outlined, detailing the coupling/decoupling operations at stations utilizing side track and its impact on the mainline capacity. A train schedule optimization model for the flexible train composition mode with online coupling/decoupling is proposed subsequently, which objective is to minimize enterprise operation cost and passenger travel cost. To implement this model effectively, an algorithm is designed and a case study is conducted. The results demonstrate that proposed method not only improves passenger service quality but also offers cost-saving benefits compared to the traditional modes of trunk/branch operation or branch independent operation. By using flexible train composition mode with online coupling/decoupling, the transportation organization of Y-type lines is enriched, provides a promising solution for achieving a more sustainable and efficient urban rail transit system.