Optimization of the scheduled transit train operating plan is investigated. By using the node partition method, the freight station nodes are transformed into a small-scale sub-network consisting of origin & destination arcs and delay arcs, thus forming a transport network of scheduled transit trains and depicting the whole process of traffic flow explicitly. So optimization of the scheduled transit train operating plan is transformed into design of a network with limitation of conjunct arcs. Taking into consideration the generalized costs of freight transport, the optimization model of the scheduled transit train operating plan is established. The model is a linear integer programming model, which covers the transit plan and makeup plan. The model is solved by Lingo 10.0. The numerical example demonstrates the feasibility of the model and algorithm.