The “customized train” is a train operated by the customized service of the passengers. The departure time, total travel time, and the travel classes are decided by passengers’ wishes. Successful operation of customized trains (CT) has a great significance to the future development in the relationship between the railway enterprise and the passenger service. In order to establish a comprehensive method for the CT operation plan, the paper proposes an intention survey method to obtain the passenger travel wishes data. Then, according to the existing timetable, the alternative set of CTs is built. The CT should satisfy the constraints of the passenger demand, the stop, and the train travel time. Based on the alternative set, a bilevel programming model for the maximum operation revenue of the CTs and minimum adjustment cost of existing timetable is established according to the passengers’ travel demands. The model also considers the constraints of actual travel time, arrival headway, departure headway, maximal adjustment time and capacity, and so on. The adjustment strategies for the train operation confliction are established. Finally, the method is proven through the analysis of actual cases, which can provide decision-making basis for future railway enterprises when operating the customized trains.