Considering the development of urban freight transport, this paper presents an operational strategy for freight transport based on the urban metro system. To improve the alignment between service capacity and transport demand under passenger and freight co-transportation (PFCT), a mixed-integer nonlinear programming model (MINLP) is developed to simultaneously optimize the train timetable (TT) and rolling stock circulation plan (RSCP), with particular consideration of flexible train composition mode and skip-stop strategies. Moreover, by introducing allocation rules for passengers and freight, the tripartite interests of operators, passengers, and freight agents are synergistically considered in the proposed model. To facilitate the model solution, a variable neighborhood search (VNS) algorithm is designed for the generation of high-quality solutions in a reasonable computational time. Finally, based on a simplified example and empirical data from the Beijing Metro Yizhuang Line, several sets of numerical examples are implemented to validate the applicability and effectiveness of the model and the approach.